Phylogenetic relationships and systematics of hares and jackrabbits (genus Lepus, Lagomorpha) are notoriously difficult. One intriguing issue is the relationship between cape hares (Lepus capensis L., 1758) and brown hares (Lepus europaeus Pallas, 1778). According to Petter, F., [1959. Elements d'une revision des lievres africains du sous-genre Lepus. Mammalia. 23, 41-67; 1961. Elements d'une revision des lievres europeens et asiatique du sous-genre Lepus. Z. Saugetierkd. 26, 30-40], these two phenotypically different taxa are conspecific. On the contrary, recent arguments were put forward to split African capensis into several species. Eleven variable microsatellite loci were used to determine the spatial genetic structure of African and South Israeli hares, currently considered cape hares, and European, Anatolian, and North Israeli hares, currently considered brown hares. Patterns of genetic differentiation of 294 hares collected at 18 locations from both species ranges were examined for accordance to the hypothesis of conspecificity or to the concept of two distinct species, the cape hare and the brown hare. Genetic variation was high (14.7 alleles/locus) and the distribution of alleles and genotypes was not homogeneous across the locations. Results from F-ST, R-ST, and G(ST)'-statistics including various AMOVA models, comparisons of private alleles with corresponding relative genetic differentiation between neighbouring populations, as well as absolute genetic differentiation patterns were by and large congruent. They all indicated that the degree of differentiation between populations belonging to the two different taxa was not higher than within the taxa. Partitioning of genetic diversity was congruent with a isolation-by-distance model, and this also suggested that the differentiation was due to geographic distances rather than the occurrence of two species-specific gene pools. Homoplasy likely had no or only a marginal effect on our results, as indicated by the standardized genetic distance G(ST)' and the presence of differently fixed alleles between the South African cape hare and all European brown hare populations at the highly polymorphic So108 locus. The results are concordant with earlier multilocus allozyme and mtDNA RFLP data, but contrast with mtDNA sequence data published earlier, that suggest distinctly separate phylogenetic units in Africa, the Near East and Europe. Nevertheless, as concluded from the microsatellite data brown hares and African cape hares might be connected via the Near East by gene flow along a network of intergrading populations that have regionally distinct gene pools. (c) 2007 Elsevier Ltd. All rights reserved.