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The genetic diversity of cultured species (e.g., plants and fish) has decreased as intensive agriculture and aquaculture have increased in recent decades. Maintaining genetic diversity in agriculture is a significant concern. To test whether aquaculture affects the genetic diversity of aquatic animals and whether traditional agriculture could help maintain genetic diversity, we conducted a meta-analysis to quantify the genetic diversity of cultured and wild populations. We also examined the genetic diversity and population genetic structure of common carp (Cyprinus carpio) in the traditional rice–fish coculture in the south of Zhejiang Province, China, using 20 microsatellite loci. The results of the meta-analysis showed a negative overall effect size of all cultured aquatic animals that were tested both when weighted by population replicate and when weighted by the inverse of variance. Aquaculture has caused a general decline in the genetic diversity of many cultured aquatic animals. The results from the survey of a traditional rice–fish coculture system in the south of Zhejiang Province of China showed high levels of genetic diversity in all 10 sampled populations (mean Na = 7.40, mean Ne = 4.57, mean I = 1.61, mean He = 0.71, and mean Ho = 0.73). Both the conventional analysis and a model-based analysis revealed a high and significant genetic divergence among the 10 sampled populations all over the three counties (FST value ranged from 0.00 to 0.13, and Nei's genetic distance ranged from 0.07 to 0.62). Populations within Yongjia and Jingning counties were also genetically differentiated, respectively. Furthermore, molecular variance (AMOVA), membership coefficients estimated by STRUCTURE, PCoA, and migration network analysis supported the findings from pairwise FST values. Our results suggest that the traditional rice–fish coculture plays an important role in maintaining the genetic diversity of carp cocultured in rice paddies and future policies should favor the conservation of the rice–fish system and raise the awareness of farmers on methods to maintain carp genetic diversity. [ABSTRACT FROM AUTHOR]