- Mutagen performs bidirectional synchronization (though it can also operate unidirectionally); rsync is unidirectional
- Mutagen uses recursive filesystem watching to avoid full filesystem rescans (whereas rsync always does a full filesystem rescan). This allows Mutagen to provide a more "real time" sync.
- Mutagen has an active synchronization loop that doesn't require manual invocation.
- Mutagen has more idiomatic Windows support.
- Mutagen doesn't require that it be pre-installed on both endpoints.
Both use differential transfers (i.e. the "rsync algorithm") for transferring individual files.
There are other differences, of course, as well as similarities. Mutagen's design is tuned for development work, rsync's design is tuned for replication. I still use rsync for archival operations on a daily basis - it's great!
