The natural communication of apes may hold clues about language origins, especially because apes frequently gesture with limbs and hands, a mode of communication thought to have been the starting point of human language evolution. The present study aimed to contrast brachiomanual gestures with orofacial movements and vocalizations in the natural communication of our closest primate relatives, bonobos (Pan paniscus) and chimpanzees (Pan troglodytes). We tested whether gesture is the more flexible form of communication by measuring the strength of association between signals and specific behavioral contexts, comparing groups of both the same and different ape species. Subjects were two captive bonobo groups, a total of 13 individuals, and two captive chimpanzee groups, a total of 34 individuals. The study distinguished 31 manual gestures and 18 facial/vocal signals. It was found that homologous facial/vocal displays were used very similarly by both ape species, yet the same did not apply to gestures. Both within and between species gesture usage varied enormously. Moreover, bonobos showed greater flexibility in this regard than chimpanzees and were also the only species in which multimodal communication (i.e., combinations of gestures and facial/vocal signals) added to behavioral impact on the recipient.