The genus Branchiostoma includes most of the 30 or so known species in the chordate subphylum Cephalochordata (lancelets). Although most lancelet species have a wide geographic distribution, they are typically rare through much of their range and are known to occur at high densities in only a few scattered localities (e.g., Lagos Lagoon, Nigeria; Xiamen and Qingdao, China; Kingston Harbour, Jamaica; and Tampa Bay, Florida) (Stokes and Holland 1996).

Molecular genetic studies have revealed a number of previously unrecognized lancelet species. For example, for many years the lancelet B. belcheri was considered to be a widely distributed species found throughout the West Pacific Ocean (including the Japanese Sea, the North and South China Seas, the Philippines, Singapore, and Indonesia). However, both morphological and genetic data now suggest that at least two different species have been treated under this name (Xu et al. 2005; Chen et al. 2007; Zhong et al. 2009). Similarly, Kon et al. (2006) found evidence of several cryptic species of non-Branchiostoma lancelets currently lumped together as Asymmetron lucayanum. Cryptic species can pose particular problems when, as in the case of Branchiostoma, the taxa are frequent subjects of investigations by researchers such as geneticists or developmental biologists with limited background or understanding of taxonomy and systematics. Fortunately, the importance of knowing the correct name of the species being studied, and the value of analyzing mtDNA sequencing as a "molecular voucher", has received more attention in recent years (Bely and Weisblat 2006; Zhong et al. 2009).