BAFF and APRIL (TNFSF13 members) are important regulatory factors for lymphocyte activation and survival. Another TNFSF13 gene that encodes a BAFF and APRIL-like molecule (BALM) was found in fish. Here we report the molecular characterization of the first TNFSF13 homolog in lampreys, a jawless vertebrate representative. In an investigation of the evolution of BAFF, APRIL, BALM and a closely related gene called TWEAK (TNFSF12), we identified an ancestral TNFSF13 gene in jawless vertebrates, but not the TWEAK gene. Hence, while TWEAK evolved in jawed vertebrates the TNFSF13 gene appeared before the divergence of jawed and jawless vertebrates. Considering the encoded protein of ancestral TNFSF13 gene in lamprey possess more BAFF like features than that of APRIL, we could notice that BAFF is present in all vertebrates, but APRIL and/or BALM independently lost in different lineages. For example, BALM is absent in all tetrapod genomes, and APRIL is lost in birds and several fish species. TWEAK is also lost in bird lineage suggesting that the genetic network of immune related genes have greatly reconstructed in birds genome. The comparative genome and transcriptome analyses suggest that an in-genomic fusion between APRIL and closely related TWEAK genes that produce a hybrid molecule called TWE-PRIL originated in mammalian lineage. Like mammalian BAFF and APRIL the ancestral TNFSF13 in lamprey exhibits a wide range of tissue and cellular expression including innate lymphoid cells and T cell-like (VLRA and VLRC) and B cell-like (VLRB) lymphocytes in early stage of vertebrate evolution.