To gain insight into the origin and evolution of asymmetries in the vertebrate habenula, we have used a combination of transcriptomic and functional approaches in a cartilaginous fish, the catshark Scyliorhinus canicula. We find that catshark habenulae harbor marked asymmetries not only in the medial habenulae as in the zebrafish, but also in the lateral habenulae, which differ extensively by their neuronal identities. Comparisons across a broad sampling of gnathostomes suggest that the latter reflect an ancestral gnathostome trait, independently lost in tetrapods and neopterygians.