Mesoplodon perrini is similar in shape to other members of this genus, with a short head and tail, a long abdomen, and a deep caudal peduncle. Like its closest relatives, Mesoplodon hectori and Mesoplodon peruvianus, it has a relatively short snout. It has a crescent-shaped blowhole with the tips facing towards the head. The mouth forms a straight line, and a series of grooves are present along the throat. As adults, M. perrini have dark gray coloration on their backs which grades to white on their undersides. The ventral side of their tail flukes is a lighter shade of grey with striations. Juvenile type specimens have a somewhat different color pattern, with a white area around the throat and a dark grey patch around the rostrum and eyes. Only the original five beached specimens have been accurately measured. The adult female was approximately 4.4 meters from nose to tail, while the adult male was 3.9 meters in length. The other three specimens were juvenile males, which were measured at 2.1, 2.2, and 2.4 meters.

Like other mesoplodont whales, male M. perrini have a set of tusk-like teeth that originate from the lower jaw. These tusks are not present in females. It is thought that they play a role in intrasexual competition, as is evidenced by a series of long, white scars along the flank of the adult male type specimen. The tusks may also help these whales distinguish individuals belonging to their species from those of similar, sympatric species.

Mesoplodon perrini is similar in appearance to a related species, M. hectori. In fact, many of the type specimens of this species were originally identified as the latter species, and were only designated as a separate species by Dalebout in 2002. Morphological characteristics that set these two species apart include minor differences in the cranium, teeth, and mandible.

Most of the characteristics that set M. perrini apart from related species are molecular. Substantial differences in mtDNA and cytochrome b form the basis for its diagnosis as a new species. Morphological similarities suggested that the closest relative of M. perrini was M. hectori. However, based on the molecular characters, Dalebout et al. concluded that its true sister species is M. peruvianus. This conclusion was later supported by analysis of nuclear actin sequences by Dalebout et al. (2004).

Range length: 2.10 to 4.43 m.

Other Physical Features: endothermic ; homoiothermic; bilateral symmetry

Sexual Dimorphism: ornamentation