To assist in the species-level identification of stranded and hunted beaked whales, we compiled a database of ‘reference’ sequences from the mitochondrial DNA control region for 15 of the 20 described ziphiid species. Reference samples for eight species were obtained from stranded animals in New Zealand and South Australia. Sequences for a further seven species were obtained from a previously published report. This database was used to identify 20 ‘test’ samples obtained from incompletely documented strandings around New Zealand. Analyses showed that four of these ‘test’ specimens (20%) had initially been misidentified. These included two animals of particular interest: (i) a Blainville’s beaked whale (Mesoplodon densirostris), the first record of this species in New Zealand waters; and, (ii) a juvenile Andrews′ beaked whale (Mesoplodon bowdoini), a species known from just over 20 strandings worldwide. A published sequence from a beaked whale product purchased in the Republic of Korea was identified as a Cuvier’s beaked whale (Ziphius cavirostris). Levels of intra- and interspecific variation were compared to determine the potential for misidentification when the database or taxonomy is incomplete. Intraspecific variation was generally <2%, and interspecific divergence was generally >4.7%. Exceptions were within-species variation in Hyperoodon planifrons, southern bottlenosed whale (4.12%), which exceeded the variation between the two species of Berardius (3.78%), and variation between the two specimens assigned to M. hectori, Hector’s beaked whale (7.14%). The latter case appears to be an error in species identification, and could represent the discovery of a new species of beaked whale.