Lancelets in Xiamen were reported as Branchiostoma belcheri in 1932, and subsequently were believed to comprise a single species. However, recent studies revealed that Xiamen lancelets actually represent two species, B. belcheri and B. japonicum. We observed thousands of lancelets from Xiamen beach to recognize these two species. Our observations showed that at least three morphological characters distinguish them: 1) the rostral fin is slightly round with the end obtuse in B. belcheri but elliptic with the end cuspate in B. japonicum; 2) the number of preanal fin-chambers is more than 80 in B. belcheri but less than 64 in B. japonicum, and the chambers are slender in the former but stout in the latter; 3) the caudal fin of B. belcheri is narrower than that of B. japonicum, and the angle between the dorsal and super-caudal fins, and between preanal and sub-caudal fins, is obtuse in B. belcheri but acute in B. japonicum. We also provide some ecological and distributional evidence to support the conclusion that there are two separate species in Xiamen waters.