Uncovering the genealogy of closely related species remains a major challenge for phylogenetic reconstruction. It is unlikely that the phylogeny of a single gene will represent the phylogeny of a species as a whole , but DNA sequence data across a large number of loci can be combined in order to obtain a consensus tree . Long sequences are needed, however, to minimize the effect of (infrequent) base substitutions, and sufficient individuals must be sequenced per species to account for intraspecific polymorphisms, an overwhelming task using current DNA sequencing technology. By contrast, microsatellites are easy to type , allowing the analysis of many loci in multiple individuals. Despite their successful use in mapping [4,5], behavioural ecology  and population genetics , their usefulness for the phylogenetic reconstruction of closely related taxa has never been demonstrated, even though microsatellites are often conserved across species [8-10]. One drawback to microsatellite use is their high mutation rate (10(-4)-10(-2)), combined with an incomplete understanding of their mutation patterns. Many microsatellites are available for Drosophila melanogaster, and they are distributed throughout the genome . Most can be amplified in the D. melanogaster species complex [12,13] and have low mutation rates [14, 15]. We show that microsatellite-specific distance measurements  correlate with other multilocus distances, such as those obtained from DNA-DNA hybridization data. Thus microsatellites may provide an ideal tool for building multilocus phylogenies. Our phylogenetic reconstruction of the D. melanogaster complex provides strong evidence that D. sechellia arose first, followed by a split between D. simulans and D. mauritiana.