Character compatibility analysis can improve the reliability of phylogenetic inference by removing ‘noisy’ sites in a sequence alignment. Two sites are ‘compatible’ if the same phylogeny can explain their character state distributions across the alignment. Incompatibility indicates homoplasy arising from back or parallel mutation. Sites are assigned compatibility scores proportional to their compatibility with other sites. Iterative removal of low compatibility sites and recalculation of compatibility scores identifies ‘cliques’ of sites that are perfectly inter-compatible. A clique with substantially more sites than all others is likely to indicate a true phylogeny. We evaluated the usefulness of this approach using three primate mitochondrial genome sequence alignments: 128 genomes from the four subspecies of the common chimpanzee, Pan troglodytes; 50 genomes from genera of the gibbon family Hylobatidae; and 87 diverse human (Homo sapiens) genomes. Sites were iteratively removed using the software package 'Shuffle' (Jermiin unpublished) and ML and MP phylogenies were estimated using the 'ape' and 'phangorn' packages in R. We predicted that for these closely related sequences compatibility analysis would provide greater confidence in well-separated branches and resolve uncertainty about poorly separated branches. As predicted, confidence in the main branches of the P. troglodytes tree, including those separating subspecies, increased; and previously uncertain gibbon lineages were resolved to be consistent with morphological and biogeographical evidence. Analysis of human sequences gave a very different result. Support for the major internal branches that separate deep African lineages collapsed, resulting in a ‘star’ phylogeny with all major lineages radiating from a single point. This unexpected result may reflect an relatively high proportion of rare variants in the human population that cause homoplasy at sites with pre-existing variation. We are currently investigating whether the pattern of variation in humans is better explained by population expansion or by directional natural selection.