The cotton aphid, Aphis gossypii Glover (Hemiptera: Aphididae), is a serious pest of citrus in northern Iran, both because of the damaged caused by its feeding and as a vector of several viruses. The genetic structure of populations of A. gossypii on citrus trees at eight localities in Iran was surveyed using seven polymorphic microsatellite loci. Of 240 individuals tested, 142 multilocus genotypes (MLGs) were identified. The presence of multicopy genotypes and negative FIS values revealed that the major mode of reproduction in northern Iran is obligate parthenogenesis. The genotypic diversity of populations ranged between 0.24 and 0.93. Considerable genotypic diversity and a high frequency of unique MLGs, confirmed there is some cyclical parthenogenesis in the region. The analysis of molecular variance revealed high intrapopulation and weak interpopulation genetic differentiation (overall FST = 0.036) among the different populations. The UPGMA dendrogram of eight populations based on Nei's genetic distance indicated two clusters: genotypes from West of Mazandaran and Guilan provinces and those from East of Mazandaran. The same results were also obtained from the STRUCTURE analysis of these populations. This information on the genetic diversity of populations of A. gossypii in northern Iran could be useful for improving the Integrated Pest Management of this aphid.