Patterns of geographic and seasonal genetic variation were assessed in natural populations of cyclically parthenogenetic rose aphids Macrosiphum rosae (L.). Nine populations were studied for a red–green colour morph and 30 allozyme loci (20 coding for enzymes and 10 for abundant proteins). Genetic variation was found at 5 of 20 enzyme loci (20%); all 10 abundant proteins proved monomorphic. The average heterozygosity was 4.3%. At some polymorphic loci genotypic frequencies showed significant deviations from Hardy–Weinberg proportions. Six local populations from Hamilton, Ontario, were studied for seasonal variation at the colour locus and at two polymorphic esterase loci (Est-2 and Est-4). All three loci showed large changes in genotypic frequencies over the season during the asexual cycle, but only for Est-4 were changes consistent among populations. This locus undergoes a regular seasonal cycle, the directional changes during the asexual phase presumably being balanced by changes during the sexual phase. The frequencies of three-locus genotypes within each locality fluctuated dramatically over the course of a season, reflecting the domination of local infestations by a few particularly successful clones. We speculate that because of such clonal competition followed by extensive migration, much of the selectively neutral variation is purged from aphid populations. The remaining polymorphic loci, which are mostly di- or tri-allelic, are subject to balancing natural selection at the gene or at closely linked loci. The Est-4 in rose aphids is an example of such a selectively maintained polymorphism.Key words: aphids, allozyme variation, seasonal variation, parthenogenesis, clonal selection, population structure.