Background: Malaria remains a pervasive public health problem in sub-Saharan West Africa. Here mosquito vector populations were explored across four sites in Mali and the Republic of Guinea (Guinea Conakry). The study samples the major ecological zones of malaria-endemic regions in West Africa within a relatively small distance. Methods: Mosquito vectors were sampled from larval pools, adult indoor resting sites, and indoor and outdoor human-host seeking adults. Mosquitoes were collected at sites spanning 350 km that represented arid savannah, humid savannah, semi-forest and deep forest ecological zones, in areas where little was previously known about malaria vector populations. 1425 mosquito samples were analysed by molecular assays to determine species, genetic attributes, blood meal sources and Plasmodium infection status. Results: Anopheles gambiae and Anopheles coluzzii were the major anophelines represented in all collections across the ecological zones, with A. coluzzii predominant in the arid savannah and A. gambiae in the more humid sites. The use of multiple collection methodologies across the sampling sites allows assessment of potential collection bias of the different methods. The L1014F kdr insecticide resistance mutation (kdr-w) is found at high frequency across all study sites. This mutation appears to have swept almost to fixation, from low frequencies 6 years earlier, despite the absence of widespread insecticide use for vector control. Rates of human feeding are very high across ecological zones, with only small fractions of animal derived blood meals in the arid and humid savannah. About 30 % of freshly blood-fed mosquitoes were positive for Plasmodium falciparum presence, while the rate of mosquitoes with established infections was an order of magnitude lower. Conclusions: The study represents detailed vector characterization from an understudied area in West Africa with endemic malaria transmission. The deep forest study site includes the epicenter of the 2014 Ebola virus epidemic. With new malaria control interventions planned in Guinea, these data provide a baseline measure and an opportunity to assess the outcome of future interventions.