Research on wild apes is not only fundamental for elucidating human origins but for their conservation as well. Despite their relative size, apes are difficult to observe in the wild prior to habituation, limiting our ability to accurately assess demography and kin relations. Non-invasive genetic sampling provides an indirect source of this information. Here, we present findings of a pilot genetic survey of a wild community of bonobos that are in the initial stages of being studied. Fifty-three fecal samples were collected over eight days near the Iyema field site in the Lomako Forest, DRC. DNA was first extracted and quantified using a qPCR assay. Samples with a sufficient amount of DNA were genotyped at 11 microsatellite loci and sexed using an amelogenin assay. Thirty-three of 53 samples yielded a sufficient amount of DNA for complete genotyping. We identified 19 individuals, including six males and 13 females. Mean allelic richness across all loci was 5.7 and expected heterozygosity was 0.69. Estimates of population size indicate between 26 and 66 individuals are present in the study area, but more than one community may be present. These results contribute to our ongoing efforts to study and monitor the bonobos at Iyema to better understand their demography, behavior, and conservation. Our study also highlights the utility of genetic analyses in pilot and survey research.