Heteroduplex mobility assays (HMAs) of a cytochrome b region were used for estimating genetic distances and phylogenetic relationships between some selected neotropical primates of the families Callitrichidae (marmosets and tamarins) and Cebidae [capuchin monkey, (Cebus apella)], and man (Homo sapiens). HMA distances were found to be strongly correlated to analogous estimates derived from DNA sequence data. Phylogenetic trees obtained by HMAs and sequence analyses showed similar topologies with almost identical intraspecific, intrageneric, and intergeneric relationships. The applicability of HMAs is assessed relative to different levels of molecular and organismal diversity.