Studies were carried out at three sites in the highlands of western Kenya (Iguhu and Mbale in Kakamega and Vihiga districts, respectively, and Marani in Kisii district) and at one site in the western Kenya lowlands (Kombewa in Kisumu district) to determine the spatial-temporal dynamics of malaria vectors and intensity of malaria transmission from June 2003 to June 2004. At the highland sites, Anopheles gambiae Giles predominated, constituting >80% of the vector species, whereas An. funestus Giles made up <20%. In contrast, at the lowland site, An. funestus made up 68% of the vector species. The mean annual indoor resting densities of An. gambiae at Iguhu were 5.0 female mosquitoes per house per night, 14.2- and 26.3-fold greater than those at Mbale and Marani. During the main transmission season, the indoor resting densities of An. gambiae increased 4.1-, 10.1-, and 5.0-fold over the dry season period in Iguhu, Mbale, and Marani, respectively. The estimated annual entomological inoculation rate (EIR) at Iguhu was 16.6 infectious bites per person per year (ib/p/yr), 1.1 at Mbale, and 0.4 at Marani. This suggests high spatial variation in vector abundance and malaria transmission intensity. At the lowland site, Kombewa, the total annual EIR was 31.1 ib/p/yr and the indoor resting densities during the transmission season increased 7.1-fold in An. funestus and 18.5-fold in An. gambiae sensu lato over the dry season. The low level of transmission in the highlands suggests that it may be disrupted by vector control methods such as residual spraying.