Cercopithecus mitis is a polytypic, pan-African guenon species with a complex evolutionary history and unresolved taxonomy. Many populations are found in remote locations leading to an incomplete survey of the species and lack of phylogenetic data. The current IUCN Red List recognizes C. mitis as one species with 16 subspecies. This study investigates the phylogenetics of two forms within the C. mitis radiation: C. m. stuhlmanni and C. m. heymansi. The C. m. heymansi population is localized and endemic to the Tshuapa-Lomami-Lualaba (TL2) Conservation Landscape in the central Congo Basin, whereas C. m. stuhlmanni has a wide distribution, from the eastern Congo Basin in DRC to western Kenya. We used a multi-locus, bi-parental approach to determine the phylogenetic relationships of these taxa. We sequenced the cytb locus of the mitochondrial genome and the TSPY gene of the Y-chromosome of samples imported from wild populations with known provenience (n=28). Incongruence was found between the gene trees for both subspecies. C. m. heymansi forms highly supported monophyletic clades in both trees, indicating that C. m. heymansi is a distinct lineage within the C. mitis radiation. C. m. stuhlmanni exhibits paraphyly in both trees, suggesting an evolutionary history shaped by historical climatic fluctuations which led to isolation followed by secondary contact. An increase in genetic data and a more complete sampling of the C. mitis radiation is needed to fully resolve the phylogenetic relationships within the species and implement taxonomic revisions to better reflect the level of diversity within the taxon.