The most efficient malaria vectors bite and rest inside houses, hence houses play a determinant role in malaria transmission. During the implementation of additional vector control tools such as larviciding, individual disease risk perception could be affected. We carried out this study to evaluate the influence of house structures, community knowledge and practices on anophelines diversity and malaria prevalence, before and during a larviciding program. The study was conducted before and during larviciding intervention in 26 districts. Indoor CDC light traps were used to collect mosquitoes. Questionnaires were administered to collect data on house characteristics and to evaluate the impact of larviciding on population knowledge and behaviour. After morphological identification, anophelines were tested by ELISA to detect infection to Plasmodium parasites. RDT was used to test the blood samples of participants. Binary analyses were used to assess the correlation between different variables. The majority of houses were made with cement walls. The most abundant anophelines was An. coluzzii, followed by An. gambiae s.s, with the _highest densities in traditional houses before the treatment in control sites, whereas, they were most abundant in modern houses in treated sites. Opened eaves and absence of ceiling exposed people to anophelines bites. Possession of LLINs before the treatment in control sites exposed people to anopheline bites while they were protected in treated sites. Infection to Plasmodium and malaria prevalence were highest in modern houses found in control sites; while in treated sites, infection to Plasmodium was highest in modern houses, but malaria prevalence was the same in both house types. People who lived in treated sites knew more about malaria prevalence and mosquito breeding sites, and the latter used fewer LLINs. Well-built houses protect people against anophelines species. The implementation of larvicide control improved the knowledge of people and decrease their personal protection against mosquito bites.