Despite a growing concern over the influence of anthropogenic disturbances on animal dispersal, not many studies have examined genetic structures in highly fragmented urban landscapes where the genetic differentiation between the subpopulations is expected to be higher than less fragmented landscapes. The goal of this study was to compare levels of genetic differentiation and diversity among populations found in relatively continuous rural habitat to populations in highly urbanized fragmented habitat. Odonata (dragonflies and damselflies) have been gathering peoples’ attention as good indicators of environmental quality. Recently, the number of each Odonata species has been declining nationwide, but some species are still commonly seen even in urban areas though habitat fragmentations could have profound influences on the genetic structure. We report the results of Amplified Fragment Length Polymorphism (AFLP) analysis for genetic structure of three damselfly species, Ishnura senegalensis, Ischnura asiatica and Cercion calamorum. Significant population genetic substructuring was found for the urban populations of C. calamorum. The observed largest Fst value on a very small spatial scale may indicate the effects of habitat fragmentation on the genetic structure.