Aphis gossypii is an aphid species that is found throughout the world and is extremely polyphagous. It is considered a major pest of cotton and cucurbit species. In Europe, A. gossypii is assumed to reproduce exclusively by apomictic parthenogenesis. The present study investigates the genetic diversity of A. gossypii in a microgeographic, fragmented habitat consisting of eight glasshouses of cucurbit crops. This analysis, which was based on the results from seven microsatellite loci, has confirmed that A. gossypii populations in southern France are primarily asexual, as only 12 nonrecombinant genotypic classes (clones) were identified from 694 aphids. Moreover, a high proportion of the aphids (87%) had one of three common genotypes. No significant correlation was found between genotypic class and host plant species. Within a glasshouse population of A. gossypii, a significant reduction in clonal diversity was observed as the spring/summer season progressed. The final predominance of a clone could result from interclonal competition. At the microgeographic level (i.e. glasshouses within a 500-m radius), significant genetic subdivision was detected and could be attributed to founder effects and the limitation of gene flow imposed by the enclosed nature of the glasshouse structure. Finally, the three common clones of A. gossypii detected in 1996 reappeared in spring 1997 following the winter extinction, together with rare clones that had not previously been seen. The probability that A. gossypii overwinters within refuges at a microgeographic scale from which populations are renewed each spring is discussed.