The genetic structure and phenotypic diversity of two populations of Cheilosia aff. longula (Diptera: Syrphidae) in Lapland, Finland, were examined using DNA sequencing, protein electrophoresis, and geometric morphometrics. The morphological identification of the species were verified using partial sequences of mitochondrial cytochrome c oxidase subunit I (COI mtDNA), and the nuclear ribosomal internal transcribed region 2 (ITS2 rDNA), and comparing the corresponding sequences of Cheilosia aff. longula and the closely related C. longula. Two and three haplotypes of the genes COI mtDNA and ITS2 rDNA were identified in the two populations. Analysis of 12 isozyme loci showed an extremely low genetic variability in the populations originating from Utsjoki and Kevo. Discriminant analysis combined with canonical variate analysis revealed inter-population divergence in wing shape. Variation among genetically diverse individuals, both within- and among studied populations was studied, and directional (DA) and fluctuating asymmetry (FA) estimated using landmarks in the framework of geometric morphometrics. It is likely that the documented DA and FA asymmetry in both wing shape and size reflects the developmental instability of the individuals studied. By using Procrustes ANOVA the locations of particular landmarks responsible for the variation in shape were determined. The decomposition of the components of variance accorded to each landmark showed that the landmarks differed in the percentage of variation they accounted for (DA, FA and variation among individuals). In the discussion the implications of the reduced genetic diversity and asymmetry in wing traits for conservation is considered.