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The genetic diversity of giant tiger prawns in relation to trace metals (TMs) pollution was analysed using 159 individuals from eight sites at the Tanzanian coast. The seven microsatellites analysed showed high degree of polymorphism (4–44 alleles). The measured genetic diversity (H o = 0.592 ± 0.047) was comparable to that of populations in the Western Indian Ocean. Apart from that, correlation analysis revealed significant negative associations between genetic diversity and TMs pollution ( p < 0.05), supporting the genetic erosion hypothesis. Limited gene flow was indicated by a significant genetic differentiation (F ST = 0.059, p < 0.05). The Mantel test rejected the isolation-by-distance hypothesis, but revealed that gene flow along the Tanzanian coast is limited by TMs pollution. This suggests that TMs affect larvae settlement and it may account for the measured deficiency of heterozygosity. This calls for strengthened pollution control measures in order to conserve this commercially important species. [ABSTRACT FROM AUTHOR]