The collective threats impacting the wild bonobo population today include: commercial poaching (for bushmeat, pets or medicinal purpose); residue of civil warfare (military sanctioned hunting, availability of modern weaponry and ammunition); human population changes (growth and movement); habitat alteration (commercial logging and agriculture, traditional slash-and-burn agriculture, increase of fallow land); and lack of education (insufficient awareness among certain urban and rural populations, and national politicians).

Commercial poaching has to be considered the most prominent threat. In some areas local taboos against bonobo hunting still exist, in others they are disintegrating due to changing cultural values associated with transient and immigrant human populations. Although commercial hunting is targeted at large-bodied ungulates and monkeys, the growing predominance of bushmeat commerce as an income-generating activity has led to increases in the number of commercial bushmeat hunters. These hunters, aided by military and local administration, are active in all areas, including those with legally protected status such as Salonga National Park. The importance of Salonga National Park as a significant reservoir of bonobos will be rapidly compromised if current hunting trends continue. Between 2003 and 2006, Hart et al. (2007) recorded evidence of hunting across the park in 51% of survey grids. Hunting pressure was considered to be high in the north and east of the park, and bonobo mortalities as a direct consequence of hunting were recorded. Bonobos are slow-breeding and thus particularly susceptible to loss caused directly by poaching or indirectly by snaring.

Infectious diseases are yet to be quantified but are undoubtedly an important threat to wild bonobo populations, and of particular concern in areas where bonobos live side-by-side with humans. The risk of transmission increases with increasing human population density as well as increasing proximity with wildlife.