BAFF (TNFSF13B/Blys) and APRIL (TNFSF13), are important regulatory factors for lymphocyte activation and survival in mammals. A BAFF/APRIL-like relative called BALM has also been identified in cartilaginous and bony fishes, and we report here a BAFF-like gene in lampreys. Our phylogenetic analysis of these genes, and a related TNFSF12 gene called TWEAK, suggest that, whereas an ancestral homologue of BAFF and APRIL was already present in a common ancestor of jawed and jawless vertebrates, TWEAK evolved early on in the jawed vertebrate lineage. Like mammalian BAFF and APRIL, the lamprey BAFF-like gene is expressed in T-like, B-like and innate immune cells. The predicted protein encoded by this BAFF-like gene in lampreys exhibits higher sequence similarity with mammalian BAFF than APRIL. Correspondingly, we find BAFF orthologues in all of the jawed vertebrate representatives that we examined, although APRIL and/or BALM orthologues are not identifiable in certain jawed vertebrates. For example, BALM is not identifiable in tetrapods, and APRIL is not identifiable in several bony fishes or in birds, the latter of which also lack a TWEAK-like gene. Our analysis further suggests that a hybrid molecule called TWE-PRIL, which is a product of an in-genomic fusion between APRIL and TWEAK genes evolved early in mammalian evolution.