One of the sharpest biogeographical transitions in the world occurs between the Indonesian islands of Borneo and Sulawesi; this transition is demarcated by Wallace's line. Macaque monkeys represent an interesting anomaly to faunal distributions in this region as they occur on both sides of Wallace's line, with Macacafascicularis, M. nemestrina and other species to the west and seven Sulawesi species to the east. We have investigated macaque evolution and dispersal in the Sunda region and Sulawesi using phylogenetic analysis of mitochondrial DNA sequences. Female philopatry of macaques, which causes sharp geographic clustering of maternally inherited mitochondrial DNA haplotypes, makes mitochondrial phytogenies particularly useful for investigating ancient patterns of dispersal. Results of this study suggest the following: (1) M. fascicularis is not a sister taxon to any species of Sulawesi macaque; (2) haplotypes of some M. nemestrina have a sister relationship to northern and central Sulawesi macaques, while haplotypes of other M. nemestrina have a sister relationship to soudiern Sulawesi macaques; (3) Sulawesi was probably colonized by macaques twice, once to the base of the northern peninsula now occupied by M. hecki and once to the southwestern peninsula now occupied by M, mama; and (4) within north/central and southern Sulawesi, patterns of dispersal are largely consistent with contemporary and past geography of the island, with the exception of a geographically discontinuous relationship between M. nigra and a portion of M. tonkeana from a region in northwest central Sulawesi.