Background: Historical studies have indicated that An. gambiae s.s. is the predominant malaria vector species in Bobo-Dioulasso the second biggest city of Burkina Faso (West Africa). However, over the last decade, An. arabiensis appears to be replacing An. gambiae s.s. as the most prevalent malaria vector in this urban setting. To investigate this species transition in more detail the present study aims to provide an update on the malaria vector composition in Bobo-Dioulasso, and also the Plasmodium infection rates and susceptibility to insecticides of the local An. gambiae s.l. population. Methods: An entomological survey was carried out from May to December 2008 in Dioulassoba and Kodeni (central and peripheral districts respectively), which are representative of the main ecological features of the city. Sampling consisted of the collection of larval stages from water bodies, and adults by monthly indoor residual spraying (IRS) using aerosol insecticides. Insecticide susceptibility tests were performed using the WHO filter paper protocol on adults emerged from larvae. PCR was used to determine vector species and to identify resistance mechanisms (kdr and ace-1 R). The Plasmodium infection rate was estimated by ELISA performed on female mosquitoes collected indoors by IRS. Results: An. arabiensis was found to be the major malaria vector in Bobo-Dioulasso, comprising 50 to 100% of the vector population. The sporozoite infection rate for An. arabiensis was higher than An. gambiae s.s. at both Dioulassoba and Kodeni. An. gambiae s.l. was resistant to DDT and cross-resistant to pyrethroids at the two sites with higher levels of resistance observed in An. gambiae s.s. than An. arabiensis. Resistance to 0.1% bendiocarb was observed in the An. gambiae s.s. S form but not the M form or in An. arabiensis. The L1014F kdr mutation was detected in the two molecular forms of An. gambiae s.s. at varying frequencies (0.45 to 0.92), but was not detected in An. arabiensis, suggesti