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Background & objectives: Malaria resurgence in highland regions of East Africa has been on increase. Thespatio-temporal distribution of larval habitats of malaria vectors determines the distribution of adult vectors,hence, disease transmission. Vector’s ecology is necessary for strategic vector control through effective plan forsource reduction. Mapping of the larval habitats is necessary for targeted control measures. The purpose of thisstudy is to assess and compare the spatial and seasonal variations in anopheline larval habitats in WesternKenya.Methods: A comparative study was conducted on spatial distribution of GPS geo-located anopheline larvalhabitats in relation to highland and lowland environments. Land use types were categorized and all potentialaquatic habitats of malaria vectors were examined in February, May, August and November 2004. Data analyseswere performed using SAS JMP software.Results & discussion: Results showed a higher percentage of Anopheles gambiae s.s. (70.9%) than An. funestus(29.1%) in highland. In the lowland, An. gambiae s.l. comprised 60.1% while An. funestus represented 39.9%.The distribution of larval breeding is confined to the valley bottom in the highland while it was dispersed in thelowland. Land use type influenced the occurrence of positive breeding habitats in the highland. In the lowland,distribution was due to seasonality. We found high proportion of potential and positive breeding sites in cultivatedswamps and farmlands at the highland site. These results suggest that swamp cultivation increases the availabilityand suitability of larval breeding habitats of malaria vectors, thus malaria transmission in the Western Kenyahighlands environment.