Atomic Swap Protocols Compared: HTLC, Submarine, Cross-Chain

Atomic Swap Protocol Overview

An atomic swap is a cryptographic technique that enables two parties to exchange assets across different blockchains or layers without trusting an intermediary. The swap either completes in full or reverts entirely: there is no state where one party has received funds while the other has not. This atomicity property distinguishes swaps from custodial bridge designs, where pooled funds create a single point of failure.

The atomic swap landscape has evolved well beyond the original on-chain HTLC design. Today, users can choose from submarine swaps bridging on-chain Bitcoin to Lightning, AMM-based cross-chain protocols like THORChain and Chainflip, and fully decentralized peer-to-peer exchanges like Bisq. Each approach makes different tradeoffs between speed, cost, trust assumptions, and asset support.

Protocol Comparison Table

The following table compares the major atomic swap protocol categories across key dimensions. Fee ranges reflect typical conditions: actual costs vary with network congestion, swap size, and pool depth.

On-Chain HTLC Atomic Swaps

The original atomic swap design uses hash time-locked contracts deployed on two separate blockchains. Party A generates a cryptographic secret, hashes it, and locks funds on Chain 1 with a timelock. Party B sees the hash and locks corresponding funds on Chain 2 with a shorter timelock. When A claims B's funds (revealing the preimage), B uses that preimage to claim A's funds. If either party abandons the swap, timelocks ensure automatic refunds.

The first successful BTC-LTC atomic swap was executed in 2017 and took roughly one hour. The core mechanics remain unchanged: on-chain HTLC swaps require multiple block confirmations on both chains, making them slow but completely trustless. No intermediary holds funds at any point.

Active implementations include Komodo Wallet (formerly AtomicDEX), which supports 500+ assets with a 0.13% taker fee and zero maker fee, and BasicSwap DEX by Particl, which runs self-hosted Docker nodes with zero protocol fees. BasicSwap is notable for supporting BTC-XMR swaps using adaptor signatures, a pair that most other protocols cannot handle due to Monero's lack of scripting capabilities. Liquidity on both platforms remains thin, limiting practical utility for large trades.

Submarine Swaps

Submarine swaps bridge on-chain Bitcoin to the Lightning Network using the same HTLC primitive. In a standard submarine swap, the user sends BTC on-chain to an HTLC, and the service provider pays a Lightning invoice using the same hash lock. When the Lightning payment settles and reveals the preimage, the provider claims the on-chain funds. Reverse submarine swaps work in the opposite direction: Lightning to on-chain.

Boltz Exchange

Boltz is the leading non-custodial Bitcoin layer bridge. It requires no accounts or KYC and supports swaps between Bitcoin mainchain, Lightning, and the Liquid Network. In March 2026, Boltz added support for USDT swaps via Arbitrum, expanding beyond pure Bitcoin pairs.

Boltz fee structure:

• BTC on-chain to/from Lightning: 0.5% + variable network fee
• Liquid to/from Lightning: 0.1% + minimal network fee (19-47 sats)
• Fees can go negative (rebates) when Boltz needs to rebalance liquidity
• Boltz Pro offers rebates up to 0.15% in certain swap directions
• Swap limit: up to 0.1 BTC per swap

For a deeper look at how submarine swaps integrate with Lightning liquidity management, see our research on Lightning Loop and submarine swaps.

Lightning Loop

Lightning Loop, built by Lightning Labs, provides submarine swap infrastructure for LND node operators. Loop Out moves funds from Lightning to an on-chain address; Loop In moves on-chain BTC into a Lightning channel. Loop is the primary liquidity management tool for the LND ecosystem, integrated into Lightning Terminal, Ride the Lightning, and ThunderHub.

Loop uses dynamic pricing: fees start around 0.05% and scale with network conditions. A 2025 upgrade introduced MuSig2 signatures that reduced on-chain swap costs. Loop Out requires a 30,000 sat prepayment deposit, and discounts are available for batched swaps where users accept longer confirmation times.

Cross-Chain AMM Protocols

Cross-chain AMM protocols use liquidity pools and validator networks to enable swaps across multiple blockchains. Unlike pure HTLC swaps, these protocols pool user-deposited assets in vaults secured by threshold signature schemes (TSS). This design enables faster swaps with deeper liquidity but introduces custodial risk in the vault layer.

THORChain

THORChain is the largest cross-chain swap protocol, supporting 13 chains including Bitcoin, Ethereum, Solana (added February 2026), XRP Ledger, BNB Smart Chain, TRON, and several others. Each pool pairs an external asset with RUNE, THORChain's native token. Swaps between two non-RUNE assets route through two pools (e.g., BTC to RUNE to ETH).

THORChain uses slip-based fees rather than fixed percentages: small swaps in deep pools cost as little as 0.1%, while large swaps in shallow pools can exceed 5%. Streaming swaps, which split large orders into sub-swaps over time, dramatically reduce slippage. A 1,000 ETH swap might cost 5% as a single transaction but only 0.05% when streamed.

THORChain's security record warrants careful review. The protocol suffered three exploits in 2021 totaling approximately $16 million, a $200 million solvency crisis in January 2025 (restructured via the TCY equity token proposal), and a $10.7 million vault drain in May 2026 caused by a GG20 TSS vulnerability. THORChain was also used as a laundering conduit in the $1.5 billion Bybit hack (February 2025) and the $293 million KelpDAO hack (April 2026). Current TVL sits at roughly $39.5 million.

Chainflip

Chainflip is a cross-chain AMM using a 100-of-150 proof-of-stake validator network with TSS-managed vaults. It supports BTC, ETH, SOL, DOT, USDC, USDT, and ERC-20 tokens without using wrapped tokens or bridges.

Chainflip's fee structure has three components: a flat 0.10% protocol fee, an LP spread of 0.05-0.15% for liquid pairs, and destination chain gas fees. Typical all-in cost ranges from 0.21% to 0.30%. For example, swapping 0.1 BTC to SOL costs approximately $15 (0.24%), while converting 5,000 USDC to USDT costs about $10.50 (0.21%). Cumulative volume reached $1.24 billion as of early 2026, with weekly FLIP token burns of approximately $80,000.

Maya Protocol

Maya Protocol is a THORChain fork that uses CACAO as its native token instead of RUNE. It supports BTC, ETH, RUNE, USDT, USDC, Dash, and several other assets. Fees run between 10 and 20 basis points (0.10-0.20%) plus outbound network fees. TVL is approximately $44 million, with average daily volume around $4 million. Maya has not experienced any protocol-level exploits, benefiting from lessons learned through THORChain's security incidents.

Peer-to-Peer Exchange: Bisq

Bisq is a fully decentralized desktop application that facilitates Bitcoin-fiat and Bitcoin-altcoin trades over a Tor-based P2P network. Unlike AMM protocols, Bisq uses 2-of-2 multisig escrow with security deposits from both parties. The Bitcoin buyer sends fiat through traditional payment rails (SEPA, ACH, Zelle, Revolut), the seller confirms receipt, and both sign the payout transaction.

Bisq charges 0.15% for makers and 1.15% for takers when paying fees in BTC (0.075% and 0.575% respectively when using BSQ tokens). Fiat sellers typically add a 3-8% premium above spot price depending on the payment method. Monthly trading volume runs around $10 million: Bisq prioritizes privacy and censorship resistance over throughput. Bisq 2, launched in March 2024, introduced a simplified "Bisq Easy" mode with reputation-based trust for small trades.

Detailed Fee and Performance Comparison

The following table provides granular fee data for specific protocols. Fees marked as "dynamic" or "slip-based" vary with swap size, pool depth, and network conditions.

Security Track Record

The security properties of each protocol category differ fundamentally. Pure HTLC swaps (Komodo, BasicSwap, Boltz, Loop) have near-zero protocol-level exploit history because there are no pooled funds to drain: each swap is an isolated contract between two parties. AMM-based protocols with pooled vaults carry significantly more risk.

THORChain has lost approximately $27 million to direct exploits across six incidents since 2021, plus a $200 million solvency crisis that required debt restructuring. The May 2026 vault drain exploited a vulnerability in the GG20 threshold signature implementation, allowing a malicious validator to reconstruct a vault private key. THORChain was also used as a laundering conduit in multiple high-profile hacks.

Chainflip and Maya Protocol have not suffered protocol-level exploits. Bisq experienced one exploit in 2020 (approximately 11 BTC lost) which was patched. By comparison, traditional cross-chain bridges lost over $329 million in the first half of 2026 alone, with bridges accounting for roughly 40% of all Web3 exploits historically. For a broader view of bridge security, see our bridge security comparison tool.

Atomic Swaps vs. Cross-Chain Bridges

The fundamental security advantage of atomic swaps over cross-chain bridges is the absence of pooled custodial funds. In an HTLC-based swap, funds move directly between counterparties: there is no smart contract vault or multisig wallet holding billions of dollars as an exploit target. Bridges have suffered over $2.8 billion in cumulative losses through 2025, with attack vectors including smart contract bugs, oracle manipulation, and private key compromise.

AMM-based swap protocols (THORChain, Chainflip, Maya) occupy a middle ground. They pool user assets in TSS-secured vaults rather than using traditional bridge messaging, which eliminates relayer and oracle attack surfaces. However, the vault model still creates concentrated targets: THORChain's May 2026 exploit demonstrated that a single malicious validator could drain a vault by exploiting the threshold signature scheme.

For Bitcoin-native use cases, Layer 2 protocols like Spark offer an alternative approach: rather than swapping across chains, users can transact in both BTC and stablecoins like USDB natively on Bitcoin without bridging to external chains at all. This eliminates both the bridge risk and the swap friction for users who want dollar-denominated payments within the Bitcoin ecosystem.

How to Choose a Swap Protocol

The right protocol depends on what you are swapping, how much, and what trust assumptions you can accept.

For moving between on-chain Bitcoin and Lightning: Boltz Exchange is the standard choice. Fully non-custodial, no KYC, and a 0.5% fee for mainchain swaps (0.1% via Liquid). Lightning Loop is the better option if you operate an LND node and need automated loop-in/loop-out liquidity management.

For cross-chain swaps between major assets (BTC, ETH, SOL, stablecoins): Chainflip offers competitive fees (0.21-0.30%) with no KYC and a cleaner security record than THORChain. THORChain provides the widest chain support (13 networks) and streaming swaps for large orders, but its repeated security incidents and use in money laundering operations represent material risk factors.

For buying Bitcoin with fiat without KYC: Bisq remains the leading option. The combined 1.3% fee plus fiat premium is higher than centralized exchanges, but Bisq provides genuine privacy and censorship resistance through its Tor-based P2P design.

For maximum trustlessness with zero protocol fees: BasicSwap DEX offers pure HTLC atomic swaps with no fees beyond network costs. The tradeoff is thin liquidity, slow speeds, and the requirement to run full nodes via Docker.

Frequently Asked Questions

What is an atomic swap in Bitcoin?

An atomic swap is a peer-to-peer exchange of cryptocurrency between two blockchains that either completes fully or not at all. The mechanism uses hash time-locked contracts (HTLCs) to ensure neither party can steal funds during the exchange. If one party fails to complete their side of the swap within the timelock period, both parties automatically receive their original funds back.

Are atomic swaps trustless?

Pure HTLC-based atomic swaps are fully trustless: no intermediary touches your funds at any point, and the cryptographic guarantees of the hash lock and timelock ensure atomicity. AMM-based cross-chain protocols like THORChain and Chainflip are semi-trustless: they remove the need for a centralized exchange but rely on validator networks to secure pooled vaults. Submarine swap providers like Boltz are non-custodial (they never hold your funds) but you do rely on the provider to complete the Lightning payment leg.

What is a submarine swap?

A submarine swap exchanges on-chain Bitcoin for Lightning Network funds (or vice versa) using an HTLC. The on-chain party locks BTC in a contract, the swap provider pays a Lightning invoice using the same hash, and when the Lightning payment reveals the preimage, the provider claims the on-chain funds. Boltz Exchange and Lightning Loop are the two primary submarine swap providers. For a detailed guide, see our research on submarine swaps explained.

How long does an atomic swap take?

Speed varies significantly by protocol type. On-chain HTLC swaps between Bitcoin and Litecoin take 30-60 minutes due to block confirmation requirements. Submarine swaps (Boltz, Loop) take 10-30 minutes for mainchain settlement, or 2-5 minutes via Liquid. Cross-chain AMM swaps (THORChain, Chainflip) typically complete in 1-15 minutes depending on destination chain confirmation times. Bisq trades involving fiat payment can take hours to days.

Which atomic swap protocol has the lowest fees?

BasicSwap DEX charges zero protocol fees: you pay only the network transaction fees on both chains. Komodo Wallet charges 0.13% for takers and nothing for makers. For submarine swaps, Boltz via Liquid is cheapest at 0.1%. For cross-chain AMM swaps, Chainflip's all-in cost of 0.21-0.30% is competitive, though THORChain's streaming swaps can achieve lower effective rates for large orders in deep pools.

Is THORChain safe to use?

THORChain has suffered approximately $27 million in direct protocol losses across multiple exploits since 2021, a $200 million solvency restructuring in January 2025, and a $10.7 million vault drain in May 2026. It has also been used as a primary laundering conduit in several major hacks, drawing attention from US Treasury sanctions. While the protocol remains operational and has paid back affected users in most cases, the repeated security incidents suggest ongoing risk. Users should not swap more than they can afford to lose.

Can I swap Bitcoin for Monero atomically?

Yes, but options are limited. BasicSwap DEX supports BTC-XMR atomic swaps using adaptor signatures rather than traditional HTLCs, since Monero lacks the scripting capabilities needed for hash-locked contracts. The COMIT network's XMR-BTC swap tool also enables this pair. Both require running local software and have thin liquidity. Most cross-chain AMMs (THORChain, Chainflip, Maya) do not support Monero.

This tool is for informational purposes only and does not constitute financial advice. Fee structures, TVL figures, and protocol details change frequently. Data is based on publicly available information as of mid-2026. Always verify current fees and security status on the protocol's official documentation before executing swaps.