Variation at 12 microsatellite loci was investigated to assess the impact of the implementation of insecticide-treated bed nets (ITNs) on the genetic structure of Anopheles arabiensis in Simatou, a village surrounded by irrigated rice fields in the Sahelian area of Cameroon. The An. arabiensis population of Simatou was sampled twice before ITN implementation, and twice after. Effective population size estimates (Ne) were similar across each time point, except for the period closely following ITN introduction where a nonsignificant reduction was recorded. Hence, we believe that ITN implementation resulted in a temporary bottleneck, rapidly followed by a demographic expansion. The genetic diversity of the population was not significantly affected since different genetic parameters (allele number, observed and expected heterozygosities) remained stable. Low estimates of genetic differentiation between the populations from Simatou and Lagdo, separated by 300 km, suggested extensive gene flow among populations of An. arabiensis in the Sahelian region of Cameroon. A decrease in the susceptibility to deltamethrin was observed following ITN introduction, but no kdr mutation was detected and a metabolic resistance mechanism is probably involved. The temporary effect of ITNs on the genetic structure of An. arabiensis population suggests that, to optimize the success of any control programme of this species based on ITNs, the control area should be very large and the programme should be implemented for a long period of time.