To assist in the species-level identification of stranded and hunted b
eaked whales, we compiled a database of 'reference' sequences from the
mitochondrial DNA control region for 15 of the 20 described ziphiid s
pecies. Reference samples for eight species were obtained from strande
d animals in New Zealand and South Australia. Sequences for a further
seven species were obtained from a previously published report. This d
atabase was used to identify 20 'test' samples obtained from incomplet
ely documented strandings around New Zealand. Analyses showed that fou
r of these 'test' specimens (20%) had initially been misidentified. Th
ese included two animals of particular interest: (i) a Blainville's be
aked whale (Mesoplodon densirostris), the first record of this species
in New Zealand waters; and, (ii) a juvenile Andrews' beaked whale (Me
soplodon bowdoini), a species known from just over 20 strandings world
wide. A published sequence from a beaked whale product purchased in th
e Republic of Korea was identified as a Cuvier's beaked whale (Ziphius
cavirostris). Levels of intra- and interspecific variation were compa
red 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 wit
hin-species variation in Hyperoodon planifrons, southern bottlenosed w
hale (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 discov
ery of a new species of beaked whale.