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Habitat fragmentation is one of the main threats to biodiversity. Barriers to dispersal caused by anthropogenic habitat alteration may affect phylogeographic patterns in freshwater mussels. Knowledge of the phylogenetic and phylogeographic patterns of unionoids is vital to inform protection of their biodiversity.Here, we assessed influences of dams and their environmental effects on the genetic diversity and population connectivity of a broadly distributed freshwater mussel, Nodularia douglasiae, in Poyang Lake Basin.The results showed high genetic diversity in areas without dams and low genetic diversity in areas with dams. High genetic differentiation and low gene flow were found among the 11 populations. Genetic variation was significantly correlated with dissolved oxygen levels.The observation of low genetic diversity in populations separated by dams indicated that those populations were subjected to genetic erosion and demographic decline because they are disconnected from other populations with higher diversity. High genetic differentiation and low gene flow among the 11 populations could be correlated with anthropogenic habitat alteration.These results indicated that anthropogenic habitat alterations have led to the decline in freshwater mussel diversity. Therefore, we recommend maintaining favourable habitat conditions and connectivity of rivers or lakes, and strengthening study of life histories with host‐test experiments to identify potential host fish species to strengthen the knowledge base underpinning freshwater mussel conservation. [ABSTRACT FROM AUTHOR]