We report here the results of the first molecular evolutionary analysis to include members of all 10 extant genera of cercopithecine monkeys. A total of 44 individuals were surveyed for ∼2.2kb of the testis-specific protein, Y-chromosome (TSPY). The TSPY sequences were subjected to parsimony analyses in PAUP 4.0, followed by tree comparison tests designed to assess existing morphological hypotheses of cercopithecine evolution. The results of these tests show that the present Y-chromosome dataset unambiguously supports: (1) monophyly of Macaca, (2) polyphyly of the mangabeys (Cercocebus and Lophocebus), (3) paraphyly of Cercopithecus, and (4) inclusion of Allenopithecus and Miopithecus in the tribe Cercopithecini. A number of unexpected Y-chromosome relationships are also discussed, including a pattern suggesting resurrection of the genus Chlorocebus for the guenons currently identified as Erythrocebus patas, Cercopithecus aethiops, and Cercopithecus lhoesti. Relative rate tests reveal significant difference in the TSPY substitution rate across numerous lineages in the tribe Cercopithecini. Because the rate differences follow no obvious phylogenetic pattern, “local” molecular clocks were not employed and divergence dates were not estimated for this tribe. In contrast, similar analysis of the Papionini reveals rate heterogeneity between a single pair of taxonomic groups: Macaca vs. the “African papionins.” Divergence dates were therefore calculated for the tribe by calibrating TSPY clocks specific to each of these two clades.