<p>The Caspian red deer <i>Cervus elaphus maral</i>, a large mammal endemic to the Hyrcanian forests in northern Iran, is particularly susceptible to habitat fragmentation, reduced genetic diversity, and climate change. To assess the genetic structure and diversity of this subspecies, a total of 58 D-loop sequences, obtained in the present study, were combined with an additional 24 sequences from GenBank and used to reconstruct the phylogenetic trees. Habitat suitability was modeled using 16 key environmental and climatic variables influencing red deer distribution. A total of 482 presence points, recorded between 2021 and 2022, were used in five individual models and an ensemble model to predict current and future habitat suitability. Projections extending to the year 2100 were generated under both optimistic and pessimistic climate scenarios. Genetic analyses revealed two major genetic groups: a distinct population in the western Hyrcanian forests and eight subpopulations in the central and eastern regions. Genetic diversity showed high haplotype diversity and low nucleotide diversity, a pattern that may be consistent with recent population expansion following historical contraction. The western population has likely experienced long-term isolation from other populations within the study area due to habitat barriers that reduce connectivity and limit dispersal. Habitat suitability modeling indicated that forests with dense vegetation comprise the main suitable habitats. Climate change projections indicate that by 2100, significant habitat loss may occur, particularly in low-lying areas near human settlements and at elevations above 2000&#xa0;m. Our ensemble projections for 2100 indicate stable suitability in the central forest, with potential increases toward the eastern and western margins. Although many of the optimal habitats are currently protected, the findings underscore the urgent need for an integrated conservation network encompassing the entire Hyrcanian region.</p>