They used to be regarded as the same species, because they look so similar. Bonobos are also known as pygmy chimpanzees, and they used to be considered a subspecies of the common chimpanzee. Right now, the scientific consensus is that the common chimpanzee, known scientifically as Pan troglodytes, is a distinct species from the bonobo, known scientifically as Pan paniscus. As one can see from their scientific names, they are considered members of the same genus. Molecular data also shows that they last shared a common ancestor about 2 million years ago. That means they have not interbred with one another for the last 2 million years. Time is not, of course, a reliable indicator of relationships, because 2 or more populations can be isolated geographically from one another for even longer periods of time than 2 million years without either changing into a different species. Studies have shown, however, that the bonobo has changed.
Bonobos differ from common chimps in being smaller, less aggressive and in their social structure. Chimpanzee society is patriarchal, which means the leader is an alpha male, whereas bonobo society is matriarchal, i.e. led by a dominant female. Male chimps beat up on the female chimps, whereas female bonobos control the males with sex. Chimpanzees are highly territorial, and males often kill males from neighboring groups. Bonobos, however, get along well with their neighbors, and bonobos are unique in spending much of their free time having sex with one another. Bonobos can do that because they live in a habitat that is more productive than those occupied by chimpanzees. Chimpanzees occupy more marginal habitats because they share their range with the larger and stronger gorillas.
Because of these differences, it is doubtful that the two different kinds of apes can successfully interbreed, even if they are can produce fertile hybrids if two individuals mated. The hybrids may behave too differently from the accepted norms in their parental groups, and may possibly be driven away from the social group. Imagine a female hybrid trying to assert dominance in a chimp society . She will most likely be beaten up by the males. Imagine a male hybrid trying to assert dominance in a bonobo group. He would probably get nowhere and won't be allowed to mate.