Various morphological characters of larvae of Aedes (Stg.) simpsoni complex collected from different localities in Uganda were studied in an attempt to characterise the species in the Ae. simpsoni complex. Morphometrics of larval characters revealed wide ranges of variation most of which separated or grouped populations. Multivariate discriminant analysis and principal component analysis discriminated between different populations. In some populations the males were fairly distinct from the females, while for some characters the populations overlapped considerably. The percent variability of each character alone is low and does not separate the species of the complex. However several characters correlated. Length of antennae (LANT), length of antennae up to Seta 1–4 (LANT4), length of head (LHEAD), and length of siphon up to position of Seta 1-S (LSIPHSET1S) showed fairly significant variability which could be used in conjunction with characters of pupae and adults to separate populations. In the wild we find anthropophilic and non-anthropophilic populations of the mosquitoes, especially in Colocasia plants, bananas (Musa sp.), Dracaenia and Ananas sp. The multivariate analysis carried out could not separate the populations into biting behaviour groups nor breeding habitat groups.