Together with the other members of the genus Babyrousa, the North Sulawesi babirusa has usually been considered a subspecies of a widespread Babyrousa babyrussa, but recent work suggests that there may be several species, differentiable on the basis of geography, body size, amount of body hair, and the shape of the upper canine tooth of the male.

In comparison, the Buru babirusa has relatively long, thick body hair, a well-developed tail-tuft, and relatively short and slender upper canines in males, while the Togian babirusa is larger, has a relatively well-developed tail-tuft, and the upper canines of the male are "short, slender, rotated forwards, and always converge".

The upper canines of the male are so curved and enlarged that they emerge through the flesh, by way of holes, to pass through the top of the snout.

In 2006, a male North Sulawesi Babirusa and a female domestic pig were accidentally allowed to interbreed in the Copenhagen Zoo.

The offspring were five hybrid piglets, two of whom died from injuries received from their mother; the remaining three (two males and one female) were found to be infertile.