Recent advances in molecular ecology allow better assessment of the role of ecological and evolutionary processes in determining the dynamics of genetic diversity in natural populations. The chukar partridge (Alectoris chukar) is abundant and continuously distributed in the mesic Mediterranean regions of Israel, becoming scarce and patchily distributed in the arid Negev Desert. This demographic transition occurs across a main environmental transition, the Northern Negev ecotone. Populations of chukars along this gradient have been shown to differ from other populations in morphology, bilateral asymmetry, and in allozyme variation. The aim of this study is to infer whether historical (i.e. secondary contact of formerly vicariant populations) or recurrent demographic events (i.e. restriction to gene flow across the ecotone) have shaped the observed patterns of genetic diversity in chukar populations in Israel. We analysed mtDNA control-region sequences in 216 chukars collected from 28 localities (five distinct geographical regions). Results show that (1) average haplotype diversity is high (h = 0.93) while haplotype divergence is low (π= 0.8%), suggesting that extant populations diversified recently; (2) mtDNA gene diversity does not significantly differ across the distribution range; and (3) haplotype distribution differs among the sampling locations (amova; P < 0.00031). Mantel test and autocorrelation analyses indicate that isolation-by-distance may explain the geographical partitioning of genetic diversity. These patterns have likely been produced by complex dynamics between past fragmentation of northern vs. intermediate and southern populations. Late Pleistocene climatic changes, fostering cycles of range contraction and expansion, may have led to genetic differentiation in allopatry, followed by restricted gene flow across secondary contact zones.