Anopheles funestus is a major vector of malaria, yet its population genetic structure, which may have major implications for malaria transmission, is poorly understood. This dissertation analyzes the population genetics of A. funestus at three geographical scales, as well as estimating an important parameter for population genetic studiesÌ¢åÛåÓthe effective population size. The total gene pool of A. funestus in Sub-Saharan Africa was shown to have a main subdivision between Western and Eastern populations, probably a manifestation of different demographic histories. In the country of Burkina Faso, in West Africa, previous population genetic studies suggested the presence of two sympatric but reproductively isolated populations, based on the observation of heterokaryotype deficits and linkage disequilibrium among inversions located on different chromosomal arms from single locales. Two chromosomal forms were hypothesized, provisionally named Kiribina and Folonzo. This hypothesis was tested first within two villages less than 1km apart in a nested spatial design to negate any affect due to geographical distance. Slight, but significant molecular differentiation was found between forms among mtDNA and microsatellites located along chromosome 3R, which contains two important inversions for chromosomal form designations. Differentiation was also found across the country; populations did not follow an isolation by distance model, but grouped populations by chromosomal form regardless of distance. Both studies gave evidence of reduced gene flow between chromosomal forms, a result of selection on chromosome 3R, recent reproductive isolation, or a combination of both. Effective population estimates were large for both forms; however, there was a substantial difference in current effective population size between the two forms which may contribute to population differentiation. Long-term effective population size was reduced in the Kiribina form along chromosome 3R indicative of selection. The results from this dissertation will provide avenues for future research with A. funestus population genetic structure not only within Burkina Faso, but across its entire species range.