A 12-month field study was conducted between April 2004 and March 2005 to determine the association between irrigated rice cultivation and malaria transmission in Mwea, Kenya. Adult mosquitoes were collected indoors twice per month in three villages representing non-irrigated, planned, and nplanned rice agro-ecosystems and screened for blood meal sources and Plasmodium falciparum circumsporozoite proteins. Anopheles arabiensis Patton and An. funestus Giles comprised 98.0% and 1.9%, respectively, of the 39,609 female anophelines collected. Other species including An. pharoensis Theobald, An. maculipalpis Giles, An. pretoriensis Theobald, An. coustani Laveran, and An. rufipes Gough comprised the remaining 0.1%. The density of An. arabiensis was highest in the planned rice village and lowest in the non-irrigated village and that of An. funestus was significantly higher in the non-irrigated village than in irrigated ones. The human blood index (HBI) for An. arabiensis was significantly higher in the non-irrigated village compared with irrigated villages. For An. funestus, the HBI for each village differed significantly from the others, being highest in the non-irrigated village and lowest in the planned rice village. The sporozoite rate and annual entomologic inoculation rate (EIR) for An. arabiensis was 1.1% and 3.0 infective bites per person, respectively with no significant difference among villages. Sporozoite positive An. funestus were detected only in planned rice and non-irrigated villages. Overall, 3.0% of An. funestus samples tested positive for Plasmodium falciparum sporozoites. The annual EIR of 2.21 for this species in the non-irrigated village was significantly higher than 0.08 for the planned rice village. We conclude that at least in Mwea Kenya, irrigated rice cultivation may reduce the risk of malaria transmission by An. funestus but has no effect on malaria transmission by An. arabiensis. The zoophilic tendency of malaria vectors in irrigated areas accounts partly for low malaria transmission rates despite the presence of higher vector densities, highlighting the potential of zooprophylaxis in malaria control.