Background & objectives: A study was conducted to characterise larval habitats and to determine spatialheterogeneity of the Anopheles mosquito larvae. The study was conducted from May to June 1999 innine villages along the Kenyan coast.Methods: Aquatic habitats were sampled by use of standard dipping technique. The habitats werecharacterised based on size, pH, distance to the nearest house, coverage of canopy, surface debris, algaeand emergent plants, turbidity, substrate, and habitat type.Results: A total of 110 aquatic habitats like stream pools (n = 10); puddles (n = 65); tire tracks (n =5); ponds (n = 5) and swamps (n = 25) were sampled in nine villages located in three districts of theKenyan coast. A total of 7,263 Anopheles mosquito larvae were collected, 63.9% were early instarsand 36.1% were late instars. Morphological identification of the III and IV instar larvae by use ofmicroscopy yielded 90.66% (n = 2,377) Anopheles gambiae Complex, 0.88% (n = 23) An. funestus,An. coustani 7.63% (n = 200), An. rivulorum 0.42% (n = 11), An. pharoensis 0.19% (n = 5), An.swahilicus 0.08% (n = 2), An. wilsoni 0.04% (n = 1) and 0.11% (n = 3) were unidentified. A subset ofthe An. gambiae Complex larvae identified morphologically, was further analysed using rDNA-PCRtechnique resulting in 68.22% (n = 1,290) An. gambiae s.s., 7.93% (n = 150) An. arabiensis and 23.85%(n = 451) An. merus. Multiple logistic regression model showed that emergent plants (p = 0.019), andfloating debris (p = 0.038) were the best predictors of An. gambiae larval abundance in these habitats.Interpretation & conclusion: Habitat type, floating debris and emergent plants were found to be thekey factors determining the presence of Anopheles larvae in the habitats. For effective larval control,the type of habitat should be considered and most productive habitat type be given a priority in themosquito abatement programm
