Anopheles moucheti is a major human malaria vector in the vicinity of slow moving rivers in the tropical forests of Central Africa. Morphological variations in natural populations of A. moucheti led to the designation of three morphological forms named A. moucheti moucheti, A. moucheti nigeriensis and A. moucheti bervoetsi. Using allozyme markers, we investigated to which extent morphological and/or geographical populations of A. moucheti were genetically differentiated. Mosquitoes were collected from four villages 20-200 km distant apart in south Cameroon, where specimens from each morphological form were found in sympatry. All populations appeared highly homogenous across both morphological type and geographic location. Significant genetic differentiation was only observed between two locations 150 km apart (F(st)=0.029; P=0.006), while no pairwise F(st) estimate between morphological forms reached statistical significance. Further evidence against any taxonomic value of this morphological classification was provided by direct observation of morphological variation within the progeny of field-collected females from all three types. Single female offspring always belonged to at least two morphologically recognised types and most often, a mixture of all three forms was observed. Our results therefore demonstrate that morphological variability within A. moucheti natural populations is not indicative of speciation. With this respect, restricted migration of individuals across river systems may be a more important factor in shaping population genetic structure of A. moucheti.