The amphioxus, also known as lancelet, is the modern representative of the subphylum Cephalochordata, providing evolutionary insight into the origin of vertebrate. Both amphioxus and vertebrate are evolving relatively slowly, and their genomes share a high level of synteny. The genome of a few species in the genus Branchiostoma have been sequenced: B. floridae, B. belcheri, and B. lanceolatum. However, though amphixous group have retained conserved morphological features for over 100 Myr, the levels of single-nucleotide polymorphisms (SNPs) is very high. Here, we assembled the genomic haplotypes of B. belcheri, B. floridae &amp B. japonicum, and re-sequenced many individuals to investigate this interest question.