In order to gain insight into the origin and mode of evolution of asymmetries in the vertebrate habenula, we have used combinations 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. Analysis of underlying mechanisms in the catshark highlight an asymmetric temporal control of neurogenesis in the medial habenulae and a central role of Wnt signaling in the elaboration of asymmetries in the lateral ones. The pathway is submitted to a highly dynamic, asymmetric regulation during habenula development, with a Nodal dependent left repression at a stage when precursors for lateral habenulae have exited cell cycles. Using a pharmacological approach during this time window, we show that Wnt activity promotes lateral right neuronal identities in the lateral right habenula, while its repression by Nodal in the lateral left habenula promotes lateral left neuronal identities. Based on comparisons of these data with those reported in the zebrafish and in the mouse, we propose that habenular asymmetry formation and diversification in gnathostomes rely on a same developmental logic, involving a conserved temporal regulation of neurogenesis, which shapes neuronal identities on both sides and is asymmetrically modified by a dynamic Wnt activity, right restricted in the ancestral state and prone to variations in time and space during evolution.