Requiem sharks (genus Carcharhinus) have previously been reported to form large aggregations around marine infrastructures in the eastern Mediterranean Sea. While this behaviour may offer fitness advantages at the individual level, the implications of extended residency at human-altered habitats for population persistence have yet to be assessed. In this work, we investigated the phylogeographic and demographic composition of sharks near a coal-fired power and desalination station in Israel. Our aim was to infer habitat use and the mechanisms underlying the aggregation behaviour, and to highlight potential conservation impacts. We sampled, measured, and released 70 individuals between 2016 and 2022 to assess genetic variability within the cytochrome C oxidase I (COI) region and to analyse the aggregation's structure based on the sharks' size and sex distribution. In addition, we performed meristic counts on a reference specimen collected dead at another power station in Israel to supplement species identification using the abovementioned techniques. Our findings indicate size-based sex segregation of adult female dusky and male sandbar sharks (Carcharhinus obscurus and Carcharhinus plumbeus, respectively), with each species comprising two COI haplotypes. In the dusky shark, one haplotype corresponded to an Indo-Pacific lineage, and the other matched an Atlantic lineage. In the sandbar shark, we observed a haplotype previously sampled in the Mediterranean Sea, the Red Sea, the Northwest Indian Ocean, and South Africa, and another haplotype that was unique to our study site and genetically closer to the former than to sequences sampled in other ocean basins. This study provides the first indication of sympatric aggregation amongst phylogeographically distinct dusky and sandbar shark lineages, suggesting that human-altered habitats in the eastern Mediterranean Sea may influence the distribution of these species. Based on the observed segregation pattern, we conclude that the site does not function as a nursery, parturition, or mating area, and discuss other plausible explanations that warrant further research. Finally, we highlight important directions for future research and the implications of our findings for management and conservation.