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We examined the population structure of sand scorpions (Paruroctonus mesaensis) by performing genetic and morphological analyses. Sand scorpions were expected to show large genetic distances among populations because they are limited to sandy habitats. However, allozyme analysis showed only moderate genetic differentiation among populations. The morphological analysis showed a geographical association among regional sites. A positive association was found among genetic, morphological and geographical distance matrices. However, the morphological distance matrix showed a higher correlation value with geographical distance than with genetic distance. This result suggests that local environmental conditions may affect scorpion morphology more than they affect genetic structure among populations. The sand scorpion population structure can be described as one with gene flow among populations in the middle of the range and increased isolation along the range boundaries. The major mechanism of genetic exchange is probably sand corridors that periodically connect different sand dune systems. As the age of the North American Sonoran Desert may be less than 10 000 years, it is also possible that isolation has not existed long enough to differentiate the populations to a greater extent.