The species-level taxonomy of this subfamily remains highly controversial, and alternative treatments than the one listed below have been suggested.

In 2011, Jessica Lynch Alfaro et al. proposed that the robust capuchins (formerly the C. apella group) be placed in a separate genus, Sapajus, from the gracile capuchins (formerly the C. capucinus group) which retain the genus Cebus. Other primatologists, such as Paul Garber, have begun using this classification.

According to genetic studies led by Lynch Alfaro in 2011, the gracile and robust capuchins diverged approximately 6.2 million years ago. Lynch Alfaro suspects that the divergence was triggered by the creation of the Amazon River, which separated the monkeys in the Amazon north of the Amazon River, who then evolved into the gracile capuchins. Those in the Atlantic Forest south of the river evolved into the robust capuchins. Gracile capuchins have longer limbs relative to their body size than robust capuchins, and have rounder skulls, whereas robust capuchins have jaws better adapted for opening hard nuts. Robust capuchins have crests and the males have beards.
• Genus Cebus
• Genus Sapajus
* Rediscovered species.

The oldest known crown platyrrhine and member of Cebidae, Panamacebus transitus, is estimated to have lived 21 million years ago. It is the earliest known fossil evidence of a mammal travelling between South and North America.

Capuchins are black, brown, buff or whitish, but their exact color and pattern depends on the species involved. Capuchin monkeys are usually dark brown with a cream/off-white coloring around their necks. They reach a length of 30 to 56 cm (12 to 22 in), with tails that are just as long as the body. On average, they weigh from 1.4 to 4 kg (3 to 9 pounds) and live up to 25 years old in their natural habitats, and up to 35 in captivity.

Capuchins prefer environments that give them access to shelter and easy food, such as low-lying forests, mountain forests, and rain forests. They are particularly abundant in Argentina, Brazil, Costa Rica, Honduras, Paraguay, and Peru. They use these areas for shelter at night and food access during the day. The canopy of the trees allows for protection from threats above, and the capuchin monkeys' innate ability to climb trees with ease allows them to escape and hide from predators on the jungle floor. This environment is mutually beneficial for the capuchins and for the ecosystem in which they inhabit. This is because they spread their seed leftovers and fecal matter across the forest floor which helps new plants to grow, therefore adding to the already abundant foliage that shelters the capuchin.