Abstract: The formerly large continuous range of brown bears in Iran has become confined to fragmented patches due to habitat conversion. Little is known about population genetic diversity, spatial genetic structure, and the consequences of geographic and ecological isolation on spatial genetic variations in Iranian bears. Literature is generally sparse on the effects of isolation by distance (IBD), isolation by resistance (IBR), isolation by environment (IBE), and ecological niche isolation on genetic differentiations of large-bodied carnivores. In this study, we investigated population structure, landscape connectivity, and genetic variations of Iranian brown bear populations using microsatellites. We tested the effects of IBD, IBR, and IBE on the genetic structure using multiple matrix randomized regression (MMRR) in an individual-based approach. A population level method based on an ecological niche modelling (ENM) framework was then used to evaluate the effect of niche divergence on genetic patterns. Bear populations displayed high genetic diversity, among the highest reported for wild brown bears. We also found a relatively significant division of brown bear populations, as well as higher effect of IBR than IBD and IBE, demonstrating the influence of landscape resistance in shaping spatial genetic variations. The results of niche comparisons among brown bear groups showed low niche overlap, and a probable phylogenetic conservatism event. We concluded that a combination of landscape resistance, ecological niche divergence, and probably mate-based dispersal behavior are affecting the gene flow of bear populations. Conservation planning of this vulnerable species should include landscape linkages to maintain gene flow among the isolated populations.