We used recently developed microsatellite DNA markers to explore the population genetic structure of the malaria vector, Anopheles moucheti. Polymorphism at 10 loci was examined to assess level of genetic differentiation between four A. moucheti populations from South Cameroon situated 65-400 km apart. All microsatellite loci were highly polymorphic with a number of distinct alleles per locus ranging from 9 to 17. Fst estimates ranging from 0.0094 to 0.0275 (P < 0.001) were recorded. These results suggest a very low level of genetic differentiation between A. moucheti populations. The recently available microsatellite loci revealed useful markers to assess genetic differentiation between geographical populations of A. moucheti in Cameroon.