We comparatively studied the dynamics of malaria transmission in the villages of Zatta (located in close proximity to an irrigated rice perimeter) and Tiémélékro (rural area with traditional agriculture), central Côte d'Ivoire. In the former village, the irrigated rice farming had been interrupted in 2003/2004 due to a farmers' conflict over land. In each village, mosquitoes were collected by human landing catches at night in sentinel houses. Anopheles gambiae was the predominant malaria vector, followed by An. funestus. In Zatta, the return to an irrigated rice farming in January 2005 was paralleled by a significant increase of the entomological inoculation rate (EIR) ranging from 38 infective bites per person per year (ib/ply) in 2003 to 295 ib/ply in 2005. In Tiémélékro high EIRs were found in 2003 (342 ib/ply) and 2005 (572 ib/ply). Our findings confirm that changes in irrigated rice agriculture influence malaria transmission dynamics, and call for control measures that are readily adapted to local eco-epidemiological settings.