Spatial and temporal variations in the distribution of anopheline larval habitats and land use and land cover (LULC) changes can influence malaria transmission intensity. This information is important for understanding the environmental determinants of malaria transmission heterogeneity, and it is critical to the study of the effects of environmental changes on malaria transmission. In this study, we investigated the spatial and temporal variations in the distribution of anopheline larval habitats and LULC changes in western Kenya highlands over a 4-year period. Anopheles gambiae complex larvae were mainly confined to valley bottoms during both the dry and wet seasons. Although An. gambiae larvae were located in man-made habitats where riparian forests and natural swamps had been cleared, Anopheles funestus larvae were mainly found in permanent habitats in pastures. The association between land cover type and occurrence of anopheline larvae was statistically significant. The distribution of anopheline positive habitats varied significantly between months, during the survey. In 2004, the mean density of An. gambiae was significantly higher during the month of May, whereas the density of An. funestus peaked significantly in February. Over the study period, major LULC changes occurred mostly in the valley bottoms. Overall, farmland increased by 3.9%, whereas both pastures and natural swamps decreased by 8.9% and 20.9%, respectively. The area under forest cover was decreased by 5.8%. Land-use changes in the study area are favorable to An. gambiae larval development, thereby risking a more widespread distribution of malaria vector habitats and potentially increasing malaria transmission in western Kenya highlands.