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Findings of regional variations in the behavioral patterns of non-human primates have led to the vigorous study of animal traditions (or culture), which contribute to a biological understanding of diversity in human cultures. Although our knowledge of behavioral variations of the bonobo (Pan paniscus) is limited compared with its sister species, the chimpanzee (P. troglodytes), variations in the prey of this species have been reported across study sites. This study describes evidence of mammals consumed by bonobos in the Iyondji site, which was established in 2010. We found evidence that Iyondji bonobos consumed duikers (Cephalophus dorsalis, C. monticola) and diurnal monkeys (Cercopithecus ascanius), which is notable because only anomalures (Anomalurus spp.) are consumed by bonobos in Wamba, a long-term study site established in 1973, located in an area adjacent to Iyondji. Moreover, bonobos do not transfer between the two populations due to the river between the sites. According to our census of duikers and diurnal monkeys, Iyondji bonobos appeared to encounter diurnal monkeys more frequently than did Wamba bonobos. Although humans have apparently had a more pronounced impact on the habitats in Wamba than on those in Iyondji, it remains unclear how such environmental conditions may have contributed to the differences in the prey consumed by bonobos in different sites. Our findings suggest that additional research at various sites could reveal the nature of the variations in the behavior of bonobos.