The black capuchin has three subspecies: Sapajus n. nigritus (nominate) and S. n. cucullatus are found in the southern part (the former eastwards, and the latter westwards) of this species' range, and both have a distinctive pair of tufts on the crown, as also suggested by the alternative common name of this species; black-horned capuchin. The last subspecies, the crested or robust tufted capuchin (S. n. robustus) is found in the northern part of this species' range (north of the Doce River), and has a median conical crest on the crown. It is sometimes considered a separate species.
The black capuchin's population number is unknown, but thought to be declining. This is due mostly to habitat loss, hunting, and the pet trade. The two southern subspecies remain relatively widespread and are rated as Near Threatened by the IUCN. The distinctive northern subspecies has a far more restricted distribution and it is considered Endangered.