Sphyrnidae haplotype species composition.

The scalloped hammerhead shark (Sphyrna lewini) is a circumglobally distributed apex predator clarified as Critically Endangered due to population declines exceeding 80%. Understanding population structure is essential for effective conservation management, yet comprehensive genetic surveys across the species’ range remain limited. We conducted a meta-analysis of all publicly available cytochrome oxidase I (COI) sequences for the family Sphyrnidae from the Barcode of Life Database (BOLD), applying a hierarchical analytical approach that examined haplotype clustering patterns across all hammerhead species. This family-level analysis enabled detection of taxonomic inconsistencies invisible to single-species queries: 18 of 1,066 samples (1.7%) carried species labels inconsistent with their haplotype assignments, with S. zygaena comprising the majority of mislabeled specimens in S. lewini haplotypes. Among 595 confirmed S. lewini samples, we identified four haplotypes forming two distinct phylogenetic groups with 94.6–96.2% sequence identity across a 184 bp COI fragment. Geographic analysis of 65 S. lewini samples with precise coordinates revealed pronounced ocean basin-scale segregation. Haplotype Group A (h1 and h4) predominated in the Indian Ocean, Atlantic basins, and South Pacific, while Group B (h15 and h2) is centered in the western Pacific. Country-level metadata for all 595 samples supported this pattern, with Indonesia harboring both groups consistent with its position at the Indian-Pacific biogeographic boundary. The rare haplotype (h15; n = 5) restricted to the North Atlantic included depositor notes indicating “possible cryptic species”. These findings reveal ocean basin-scale partitioning in S. lewini with implications for defining management units in this threatened species.