Microsatellites are defined as tracts of tandemly repeated short DNA sequences. Polymorphisms in this class of DNA are currently being used to generate a genetic map of the mosquito Anopheles gambiae. In the present study we explore the potential of microsatellites as a tool for studying the genetic structure of natural populations of this malaria vector. Genetic polymorphism at twenty enzyme coding gene loci and eleven microsatellite DNA loci was surveyed in a population of An. gambiae from Mali, West Africa. All of the microsatellite loci surveyed were polymorphic, as compared to 40% of the isozyme loci. The mean heterozygosity for the isozyme loci was only 0.097 (+/- 0.0035), but for the microsatellite loci it was 0.732 (+/- 0.060). The pattern of variability was very different between isozymes and microsatellites. Typically, at an isozyme locus a single allele occurred at a frequency > or = 0.75, whereas at microsatellite loci the most common allele had a frequency < 0.50. We conclude that microsatellites provide a rich source of genetic polymorphisms for the study of the population genetics of An. gambiae and are in many ways superior to isozymes for this purpose. We discuss the potential for utilizing genetically mapped microsatellite loci to explore the effect of chromosomal inversions on the distribution of genetic polymorphisms in An. gambiae.