BACKGROUND: Blood-meal sources of malaria vectors affect their capacity to transmit the disease. Most efficient malaria vectors prefer human hosts. However, with increasing personal protection measures it becomes more difficult for them to find human hosts. Here recent malaria vector blood-meal sources in western Kenya highlands were investigated. METHODS: Adult mosquitoes resting indoors, outdoors and exiting through windows were collected in three study areas within the western Kenya highlands from June 2011 to June 2013. A census of people, livestock and of insecticide-treated nets was done per house. Mosquito blood-meal sources were determined as human, goat, bovine or chicken using enzyme-linked-immunosorbent assays. RESULTS: Most (86.3 %) households possessed at least one bed net, 57.2 % had domesticated animals and 83.6 % had people sharing houses with livestock at night. Most (94.9 %) unfed malaria vectors were caught exiting through windows. Overall, 53.1 % of Anopheles gambiae sensu stricto obtained blood-meals from humans, 26.5 % from goats and 18.4 % from bovines. Single blood-meal sources by An. gambiae s.s. from humans were 26.5 %, 8.2 % from bovines and 2.0 % from goats. Mixed blood-meal sources by An. gambiae s.s. identified included: 24.5 % human/goat, 10.2 % human/bovine, 8.2 % human/bovine/goat and also 8.2 % bovine/goat. One An. arabiensis mosquito obtained blood-meal only from humans. CONCLUSION: An unusually high frequency of animal and mixed human-animal blood meals in the major malaria vector An. gambiae s.s. was revealed in the western Kenya highlands where bed net coverage is above the WHO target. The shift in blood-meal sources from humans to livestock is most likely the vectors' response to increased bed net coverage and the close location of livestock frequently in the same house as people at night. Livestock-targeted interventions should be considered under these circumstances to address residual malaria transmission.