Perrin's beaked whale was described as a new species in 2002 by Dalebout et al. based on five animals stranding on the coast of California between 1975 and 1997, which were initially identified as other species. The common and specific names of "Mesopledon perrini" are a tribute to cetologist William F. Perrin. As of May 2019, only six specimens have ever been examined. The first two specimens were found stranded on the California coast in May 1975, other specimens were found in 1978, 1979, September 1997 (a strong El Niño year), and October 2013. The first four individuals were initially identified as Hector's beaked whales ("Mesoplodon hectori"), but the mtDNA sequence database of beaked whales revealed the specimens were genetically distinct. The fifth was assumed to be a neonate Cuvier's beaked whale ("Ziphius cavirostris").