<p>This study focuses on describing and assessing the genetic structure and diversity among populations, as well as constructing a dendrogram of genetic similarity of the hawksbill turtle (<i>Eretmochelys imbricata</i>) in four nesting habitats along the Persian Gulf: Kharkoo, Nakhiloo, Shidvar, and Ommolgorm. For this purpose, we collected 14 samples of dead hawksbill turtle hatchlings from these locations and utilized six ISSR markers for genetic analysis. Results showed that 71% of the observed polymorphism was related to within-population diversity, while 29% was linked to among-population diversity. The percentage of polymorphism at the loci (AG)8 C, (AG)8G, (GA)8AC, (GA)8AG, (GACA)4, and (GTG)5GC for the Kharkoo, Nakhiloo, Ommolgorm, and Shidvar nasting group was 0%, 4.35%, 8.7%, and 30.43%, respectively. In the resulting dendrogram of genetic similarity, individuals from each nesting group were placed on separate branches, with different nesting groups situated close to or far from each other based on genetic similarity. According to population structure analysis, the Kharkoo and Shidvar nesting groups formed one subpopulation, whereas the Nakhiloo and Ommolgorm populations constituted separate groups. Hawksbill turtles are typically observed along these shores for 3 to 4 months during the nesting season, after which they emigrate to feeding areas far from the nesting habitats. The natal homing hypothesis states that female hawksbill turtles return to the nesting habitat where they were born, often years later. This hypothesis supports the genetic findings obtained from our study samples.Therefore, each of these habitats is critically important for conservation, and any adverse conditions affecting them could lead to the loss of unique genetic compositions and bring the population of this species one step closer to extinction.</p>