Background: Baseline information that is essential for determining the areas to target with larval control includes estimates of vector diversity and larval habitat preferences. Due to a lack of such information in Baringo County, Kenya, this study assessed species diversity and larval habitat preference of potential mosquito vectors of Rift Valley fever (RVF) and malaria. Methods: Mosquito larvae were sampled from nine types of larval habitats and were identified morphologically. Species diversity was estimated by the Shannon’s diversity index while larval habitat preference by RVF and malaria vectors was determined by ANOVA. Results: A total of 7724 immature mosquitoes comprising 17 species belonging to four genera, namely Anopheles, Culex, Aedes and Mansonia, were identified. Among the 17 species, three Anopheles species are responsible for malaria transmission: An. gambiae (s.l.), An. funestus (s.l.) and An. pharoensis. Rift Valley fever vectors included Mansonia spp. and Culex spp. The highest Shannon’s diversity index was observed during the cold dry season (H = 2.487) and in the highland zone (H = 2.539) while the lowest diversity was recorded during the long rain season (H = 2.354) and in the riverine zone (H = 2.085). Ditches had the highest mean number of Anopheles larvae (16.6 larvae per sample) followed by swamp (12.4) and seasonal riverbed (10.7). Water pit and water pan had low mean numbers of Anopheles larvae (1.4 and 1.8, respectively) but relatively high mean numbers of culicines (16.9 and 13.7, respectively). Concrete tank was the least sampled type of habitat but had highest mean number of culicine larvae (333.7 l) followed distantly by water spring (38.9) and swamp (23.5). Overall, larval habitats were significantly different in terms of larval density (F(8,334) = 2.090, P = 0.036). Conclusions: To our knowledge, the present study reports culicine larval species diversity in Baringo for the first time and the most preferred habitats were concrete tanks, water springs and swamps. Habitats preferred by Anopheles were mainly riverbed pools, ditches and swamps. Environmental management targeting the habitats most preferred by potential vectors can be part of integrated vector control in Baringo, especially during dry seasons.

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