Background: Malaria control in Kenya is based on case management and vector control using long lasting insecticidal nets (LLINs) and indoor residual spraying (IRS). Irrigation practices maintain vector population and thus transmission during dry season. Development of insecticide resistance further compromises the effectiveness of insecticide-based vector control programs. The aim of this study was to assess the status and mechanism of insecticide resistance in malaria vectors in irrigated and non-irrigated areas in western Kenya and the contribution of public health interventions and agriculture to insecticide resistance. Methodology: The study was carried out in 2018–2019 in Homa Bay County, western Kenya. Anopheline larvae were collected in irrigated and non-irrigated fields, reared to F1 adults and 2-5 day-old female vector mosquitoes were subjected to standard WHO insecticide susceptibility tests. The test specimens were then screened for knock-down resistance, kdr alleles, and analyzed for presence of acetyl-cholinesterase inhibiting enzyme; angiotensin-converting enzyme (Ace-1) genes. All field-collected samples were preserved for species identification by polymerase chain reaction. To ascertain the probable cause of vector resistance to insecticides, a questionnaire was administered to farmers, households and veterinary officers in the study area to assess the use of public health and agricultural insecticides/pesticides.Results: Anopheles arabiensis was the only species tested in irrigated (100%, n=154) area and predominant species in the non-irrigated areas (97.5%, n= 162) and the rest were An. gambiae sensu stricto. In 2018, susceptibility was observed in the vector species in the irrigated area and phenotypic resistance in the non-irrigated area while in 2019, phenotypic resistance was observed from all areas However, susceptibility to malathion (mortality 100%), DDT (98.98%-100%) and PBO- deltamethrin (100%) was observed. Molecular analysis of the vectors from the irrigated and non-irrigated areas revealed low levels of leucine- serine/ phenylalanine substitution at position 1014 (L1014S/ L1014F) with a mutation frequencies of 1%-16%, and almost zero mutation in Ace-1R gene (0.7%). In addition to very high coverage of LLINs impregnated with pyrethroids and IRS with organophosphate insecticides, pyrethroids were the predominant chemical class in pesticides used for crop and animal protection.Conclusion: Extensive use of pyrethroids in agriculture and public health could have resulted in the initial development of insecticide resistance. The susceptibility of these malaria vectors to organophosphates and PBO synergist in pyrethroids offers a promising future for IRS and ITN based vector control interventions.