In the chapter, we discuss the evidence about the origins of the vertebrate adaptive immune system. Amphioxus is very likely to have lymphocyte-like cells and related transcription factors and to have an antecedent MHC-linked genomic region. More importantly, a novel DNA transposon discovered in amphioxus has proven to be the long-sought RAG transposon, which is supposed to give rise to the later RAG1 and RAG2 genes that mediate the Ig/TCR somatic recombination. © 2016 China Science Publishing & Media Ltd. Published by Elsevier Inc.