The distributions of anopheline larval habitats were aggregated in valley bottoms in Kenya in both the rainy and dry seasons, although the degree of aggregation was higher in the dry season than in the rainy season. Larvae of the Anopheles gambiae complex larvae were found more frequently in habitats in farmlands and pastures. However, An. funestus larvae were found more frequently in natural swamps and pastures. Canopy cover was the only variable significantly associated with the occurrence of the An. gambiae complex and An. funestus. The average canopy cover was significantly less in the habitats with the An. gambiae complex and An. funestus larvae than those without the anopheline larvae. Thus, land cover types and topographic features showed important effects on the distribution of anopheline larval habitats. These results suggest that clearing riparian forests would improve growing conditions of the An. gambiae complex and An. funestus larvae in Kenyan highlands.