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This study collected baseline data on malaria vectors to characterize the drivers and the factors of persistent malaria transmission in two villages in the western part of Burkina Faso. Mosquitoes were collected in each village using the Human landing catch and pyrethrum spray catch and identified using the morphological keys. Molecular analyses were performed for the identification of An. gambiae complex species, the detection of Plasmodium infection and kdr-995F mutation. Anopheles mosquito larvae were also collected in the same villages, reared to adult's stage for the WHO tube and cone tests performing. The physical integrity of the LLINs already used by people in each village was assessed using the proportional hole index (pHI). An. gambiae s.l. was the main malaria vector accounting for 79.82% (5560/6965) of all collected mosquitoes. The biting pattern of An. gambiae s.l. was almost constant during the survey with an early aggressiveness before 8 p.m. and later biting activity after 6 a.m. The EIR varied from 0.13 to 2.55 infected bites per human per night (average: 1.03 infected bites per human per night). An. gambiae s.l. populations were full susceptible to Chlorpyrifos-methyl (0.4%) and Malathion (5%) with high kdr-995F mutation frequencies (>0.8). The physical integrity assessment showed high proportion of good nets in Santidougou compared to those collected in Kimidougou. This study highlighted a persistence of malaria transmission despite the intense use of vector control tools as LLINs and IRS by correlating mosquito biting time and human behavior. It provided a baseline guide for the monitoring of the residual malaria transmission in sub-Saharan Africa and encouraging the development of new alternative strategies to support the current malaria control tools. [ABSTRACT FROM AUTHOR]