Mesoplodon perrini, a new species of beaked whale is described on the basis of five animals stranded on the coast of California (between 32°55′N, 117°15′W and 36°37′N, 121°55′W) from May 1975 to September 1997. Four of these animals were initially identified as Hector's beaked whales M. hectori based on cranial morphology (Mead 1981). A fifth specimen was initially identified as a neonate Cuvier's beaked whale Ziphius cavirostris based on external features. These specimens were first recognized as representatives of an undescribed species through phylogenetic analysis of mitochondrial (mt) DNA control region and cytochrome b sequence data. Although similar morphologically, the genetic data do not support a close evolutionary relationship between M. perrini and M. hectori. Instead, these data suggest a possible sister species relationship with the lesser beaked whale M. peruvianus. Sightings of two small beaked whales off California in the 1970s which were tentatively identified as M. hectori are also likely to be M. perrini. We suggest that M. hectori is confined to the Southern Hemisphere, while M. perrini is known to date only from the North Pacific.