From about 250 Cirsium spp., only two Aceria spp. (Acari: Eriophyoidea) have been described, Aceria anthocoptes (Nal.) and Aceria cirsii Pet. B. & Shi. Host specificity, which generally characterizes eriophyoid mites, potentially leads to speciation, so we may expect more than two Aceria spp. and/or other infraspecific taxa. Furthermore, studies on host-related variability in the morphology of Aceria mites are generally lacking. The purpose of this study was to investigate quantitative morphological traits of five Aceria populations inhabiting five Cirsium spp. in Serbia. MANOVA analysis revealed significant differences in 23 commonly used morphological traits as well as four additional traits related to the prodorsal shield design. In addition, the most important qualitative traits using scanning electron microphotographs were studied in order to clarify phenotypic differences among five Aceria spp. Discriminant analysis identified eight traits that significantly differentiate five populations. UPGMA cluster analysis of the squared Mahalanobis distances indicates that A. cirsii was morphologically the most divergent, while A. anthocoptes populations from Cirsium arvense and Aceria sp. from Cirsium heterophyllum were isolated from the branch clustering Aceria spp. populations from Cirsium eriophorum and Cirsium creticum. Analysis of qualitative traits using SEM confirmed results obtained from the analysis of morphometric features.