The chromosomal polymorphism of Anopheles funestus sensu stricto from Angola was analyzed from indoor-resting samples collected in 11 peri-urban and rural sites of the Luanda and Huambo Provinces, which are > 450 km apart and have distinct eco-climatic conditions. Five polymorphic paracentric inversions were observed (scored chromatids range = 202 to 248): 2R a , 2R h , 3R a , 3R b , and 3L a . Inversions 3R b and 3L a were highly polymorphic; the 2R a and 3R a arrangements were absent in Luanda. No significant departures from Hardy-Weinberg and linkage equilibria were found at the locality, commune, or province level (sites ≤ 50 km from each other), indicating panmixia in each locale. Pooling the Luanda and Huambo samples produced a Wahlund effect, with significant levels of genetic differentiation suggestive of restrictions to gene flow due to geographic distance. The observation that differentiation was limited to inversions 2R a and 3R a can also be interpreted as divergent selection acting on these chromosomal regions between populations from the two provinces.