We examined 3747 teeth from 134 hares (Lepus sp.) collected at 46 sites in Israel to test whether variation in epigenetic occlusal characters was linked to ecogenetic or phylogenetic factors. Collection sites encompassed a wide range of ecogeographical and climatic regimes. We compared data from Israeli hares with occlusal characters of 160 cape hares L. capensis from East Africa and 68 brown hares L. europaeus from central Europe. Only three teeth (I1, I2, M3) did not show occlusal variation. Thirty-eight occlusal characters were derived from dental variants by dichotomous (0/1) scoring. Absence of association of character states among characters of single teeth indicated a lack of morphotypes. Epigenetic differentiation among hares from northern, central and southern Israel, and the two East African, and two central European samples, was revealed by pairwise C. A. B. Smith's ‘mean measures of divergence’ (MMD), based on frequencies of character states. Cluster analyses of MMD values revealed little epigenetic differentiation between northern and southern Israeli hares, but greater differentiation between central European and East African hares. Concordance of the MMD matrix with linear geographical distances among sampling regions was demonstrated by a Mantel test. No frequencies of character states exhibited significant changes across the climatic parameters among hares from northern and southern Israel. But the individual folding index, which expresses the degree of enamel on the occlusal surface, slightly decreased from north to south. Our results support a phylogenetic interpretation of occlusal character variation. Despite distinct differences in external appearance, hares from northern and southern Israel probably comprise a single species that encompasses two closely related geographical populations with a probable area of overlap. Israeli hares are intermediate between European brown hares and East African cape hares, with a slightly closer relationship to the cape hares.