With abundant and easily observable species, the use of synapomorphic characters to assign observed individuals to a particular species, is a reasonably effective approach to taxonomy, at least in its rudimentary phase.However, the translation of this approach to rare species with elusive life histories, such as the Hector's beaked whales, can be problematic for many reasons. Also, the usefulness of whole or partial "voucher" specimens in private collections to assign taxonomic difference based on morphology is equally susceptible to inaccuracy, and additionally can lead to unethical acquisition methods, such as illegal hunting of a rare species. Therefore, the accurate and ethical approach to the taxonomic study of rare and elusive species, such as are found within the mysterious, deep-diving Ziphiidae family, is a molecular phylogenetic taxonomic methodology. This method has yielded insightful discovery in recent studies of the Ziphiidae family. Between 1975 and 1997, five beaked whales were found stranded in Southern California; based on morphology, four were identified as members of M. Hectori and one was identified as a member of Ziphius cavirostris. This discovery was puzzling, because although the suspected range of Ziphius cavirostris was met by the stranding location, M. Hectori was thought to be restricted solely to the Southern Hemisphere. mtDNA sequencing of the sample species revealed that all five individuals could be genetically distinguished from all other members of Ziphiidae family, including the two species they were previously identified as. They were subsequently classified as a new species, Perrin's beaked whale (M. Perrini). More recent phylogenetic analyses of nuclear actin sequences substantiated the validity of this classification, as a distinct 34 base-pair deletion was found in the allele, screened across all species, of the two M. perrini samples in particular.

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