BackgroundThere was no record of Aedes aegypti in Yunnan Province, China, until 2002, but this species is now continuously found in nine cities (or counties). Until now, little was known about the genetic diversity and population structure of this invasive species. Thus, a detailed understanding of the invasion strategies, colonisation and dispersal of this mosquito from a population genetics perspective is urgently needed for controlling and eliminating this disease vector.MethodsThe genetic diversity and population structure of Ae. aegypti communities were analysed by screening nine microsatellite loci from 833 Ae. aegypti mosquitoes sampled from 28 locations in Yunnan Province.ResultsIn total, 114 alleles were obtained, and the average polymorphic information content (PIC) value was 0.672. The value of the alleles per locus ranged from 2.90 to 5.18, with an average of 4.04. The value of He ranged from 0.353 to 0.681, and the value of Ho within populations ranged from 0.401 to 0.689. Of the 28 locations, two showed significant departures from the Hardy-Weinberg equilibrium (HWE) with P-values less than 0.05, and a bottleneck effect was detected among locations from Ruili and the border areas with the degree of 60% and 50%, respectively. Combined with the F-statistics (FIT = 0.222; FCT = 0.145), the analysis of molecular variance (AMOVA) revealed that there was substantial molecular variation among individuals, accounting for 77.76% of the sample, with a significant P-value (<0.0001). The results suggest that genetic differences in Ae. aegypti originated primarily among individuals rather than among populations. Furthermore, the STRUCTURE and UPGMA cluster analyses showed that Ae. aegypti from the border areas were genetically isolated compared to those from the cities Ruili and Jinghong, consistent with the results of the Mantel test (R 2 = 0.245, P < 0.0001).ConclusionsContinuous invasion contributes to the maintenance of Ae. aegypti populations’ genetic diversity and different invasion accidents result in the genetic difference among Ae. aegypti populations of Yunnan Province.Electronic supplementary materialThe online version of this article (doi:10.1186/s13071-017-2213-6) contains supplementary material, which is available to authorized users.