In total, 324 Anopheles funestus Giles specimens collected from seven houses in western Kenya and seven in coastal Kenya were scored for their paracentric chromosomal inversions with the aim of determining the level of genetic differentiation based on these inversions. Houses in each area were within a 2-km radius. The two areas are ≈700 km apart. Only inversions 2a, 3a, 3b, and 5a were found to be polymorphic. Levels of polymorphism varied greatly between inversions. There were no significant deviations from Hardy-Weinberg expectations for samples from individual houses at one site or when data for houses in each area were pooled. Overall, the level of differentiation between western and coastal Kenya was significant, suggesting that the two populations are genetically isolated. Results based on inversion 2a alone were, however, not consistent with this conclusion. Founder effects and selection against the 2a inversion are discussed as possible explanations for this discrepancy.