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Water-dependent species inhabiting desert regions seem to be a contradiction in terms. Nevertheless, many species have evolved survival strategies for arid conditions. In Odonates (dragonflies and damselflies), both larvae and adults require very different and complex water-associated habitat conditions. The present study investigates the genetic diversity, population structure and dispersal patterns of a desert inhabiting odonate species, the Red-veined Dropwing dragonfly, Trithemis arteriosa. Eight populations from the arid Namibia and four population sites in the more tropical Kenya were compared by using nine microsatellite loci, one non-coding nuclear fragment and the mtDNA fragment ND1. Microsatellite analyses as well as the nuclear fragment reveal a high allelic diversity in all populations with almost no genetic sub-structuring. In contrast, ND1 sequence analyses show sub-structuring and-with two exceptions-only private haplotypes. The conflicting patterns of nuclear versus mitochondrial markers suggest a male-biased dispersal in this species. Results indicate that male dispersal is dependent on the environmental stability of the habitat, while females are philopatric. This life history adaptation would allow females to save energy for mating and oviposition in the demanding environment of a desert region. The results give direct insights into the dispersal pathways of a desert-inhabiting, strongly water dependent flying insect.