This study aimed study the genetic diversity and differentiation of Asian horseshoe crab Tachypleus gigas (Müller, 1785) populations across three distinct locations in Peninsular Malaysia: Kampung Pasir Puteh (KPPuteh), Kuala Sungai Ayam (KSAyam), and Kampung Pulau Sayak (KPSayak). A total of 28 individuals were collected, and their genetic structure was analyzed using starch gel electrophoresis. The study employed multiple buffer systems optimized for separating 20 different enzymes, each contributing to understanding the genetic variability within and between populations. The findings of this study, which revealed significant genetic differentiation, particularly between populations in polluted and less impacted environments, as reflected by high FST values and distinct clustering in the UPGMA dendrogram, are of paramount importance. The results indicate that environmental factors, especially metal-polluted sites at KPPuteh and KSAyam, have played a critical role in shaping the genetic structure of these populations. Populations from the two polluted sites, exhibited higher genetic diversity and greater deviations from Hardy–Weinberg equilibrium, suggesting localized selection pressures. Conversely, from a less polluted site, the unpolluted site at KPSayak population showed lower genetic variability and was genetically distinct from the others. These findings underscore the importance of considering environmental influences in conservation strategies for T. gigas, highlighting the need for site-specific management to preserve genetic diversity and ensure long-term survival of the species.