Clonal diversity of obligately parthenogenetic Daphnia pulex was examined in 147 ponds at 13 sites near Churchill, Manitoba. Cellulose acetate electrophoresis of four polymorphic loci allowed the detection of 16, multi-locus genotypes (clones). The three most common clones accounted for 86 per cent of the 3291 animals surveyed. An average of 1·5 clones coexisted in single ponds, while an average of 3·8 clones was present at each site. Fifteen of the sixteen clones show unbalanced electromorph phenotypes at one or more loci suggesting that they are polyploids. There was significant spatial autocorrelation of the distribution of certain clones within a given site on a scale of tens of metres. Clinal patterns in clone distributions were often found. No significant between-site spatial autocorrelation was found on a scale of 0–20 kilometres, although between-site heterogeneity of clonal frequencies was frequently seen. Microgeographic heterogeneity of D. pulex clones at Churchill is influenced by salinity gradients on a scale of tens of meters. Mechanisms that might influence the clonal structure of this apomictic complex are discussed.