Genetic Diversity and Impacts of Stocking on <i>Cyprinus carpio</i> Populations in Türkiye: Insights From Mitochondrial, Nuclear, and Microsatellite Markers

ABSTRACT Understanding genetic diversity and population structure is essential for the sustainable management of widely stocked freshwater species such as common carp ( Cyprinus carpio ). In this study, we conducted a comprehensive genetic assessment of C. carpio populations across Türkiye using mitochondrial (COI), nuclear (RAG1), and microsatellite markers. A total of 464 individuals from 29 sampling locations, including one hatchery population, were analyzed. Mitochondrial (COI) and nuclear (RAG1) markers showed low to moderate haplotype diversity, with star‐like haplotype networks dominated by a few common haplotypes, consistent with demographic expansion and widespread gene flow. Microsatellite data revealed reduced genetic diversity, with mean observed heterozygosity of 0.37 and a broad range of inbreeding coefficients ( F IS = −0.765 to 1). Analysis of molecular variance indicated that most genetic variation occurred within populations (64.12%), with comparatively weaker differentiation among populations ( F ST = 0.17). Bayesian clustering and multivariate analyses showed no clear population sub‐structuring, and Mantel tests detected no significant correlation between geographic and genetic distances. Overall, the genetic patterns observed are consistent with long‐term stocking practices, repeated use of limited broodstock, and anthropogenic translocations, which may contribute to genetic homogenization across populations. Although common carp is not currently considered threatened in Türkiye, maintaining genetic diversity remains important for sustainable aquaculture, fishery productivity, and long‐term population resilience. These findings highlight the need for continued genetic monitoring and more informed broodstock management to support the long‐term genetic integrity of wild and cultured C. carpio populations.