Comments: There has been some disagreement as to whether the recognition of subspecies is warranted (see reviews by Wilson et al. 1991 and Bodkin and Kenyon 2003). A recent range-wide review of geographic variation of skull characters concluded that three subspecies should be recognized: E. lutris lutris from Asia to the Commander Islands, E. l. nereis in California, and E. l. kenyoni in Alaska (Wilson et al. 1991). The subspecific taxonomy suggested by morphological analyses is largely but not completely supported by subsequent molecular genetic data. Analysis of mitochondrial DNA (mtDNA) variation among eight geographically isolated populations identified four major groups (Cronin et al. 1996, Scribner et al. 1997). The haplotype frequency in the Commander Island population of E. l. lutris is more similar to that observed in the Aleutian-Kodiak grouping, E .l. kenyoni, than to the Asian populations of subspecies E. l. lutris, with which it was aligned by skull morphology. Additionally, the Prince William Sound population differs from the other Alaska populations in haplotype frequency. Subspecies nereis appears to have monophyletic mtDNA, but lutris and kenyoni do not (Cronin et al. 1996). The low level of divergence of sequences of haplotypes on mtDNA suggests that there are no major phylogenetic breaks or long-term barriers to gene flow among sea otter populations (Cronin et al. 1996).
Lidicker and McCollum (1997) examined allozyme variation and found that despite historical population depletion, otters from California have suffered only a small loss in genetic variability. MtDNA data also indiciate that population bottlenecks probably did not result in major losses of genetic variation in individual populations or the species as a whole (Cronin et al. 1996). However, based on microstatellite DNA and mtDNA, Larson et al. (2002) reported that the levels of genetic diversity observed within sea otter populations were relatively low when compared with other mammals and may be the result of fur trade exploitation.