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The present study investigated the effect of ε-Polylysine on bacterial communities, sensorial, and chemical properties [total volatile basic nitrogen (TVB-N), biogenic amines, and breakdown products of adenosine triphosphate] of bighead carp ( Aristichthys nobilis ) fillets stored at 4 ± 1 °C. Bacterial communities were explored by the culture-dependent method and the high-throughput sequencing targeting on 16S rRNA genes. The results showed that the major genera in spoiled control samples were Aeromonas , Pseudomonas , Shewanella , and Acinetobacter . ε-Polylysine inhibited the growth of Pseudomonas , Shewanella , and Acinetobacter . Consequently, Aeromonas and Janthinobacterium were dominant in spoiled treated samples. The sensorial shelf-life of the control and treated groups were 8 days and 10 days, respectively. Furthermore, due to the inhibitory effect of ε-Polylysine on bacteria, chemical changes of the treated group were slower, reflecting as lower concentrations of TVB-N, putrescine, cadaverine, and hypoxanthine, and higher contents of inosine 5′-monophosphate and hypoxanthine riboside at the end of storage. In conclusion, ε-Polylysine altered the bacterial communities and delayed quality deterioration of bighead carp fillets during chilled storage. [ABSTRACT FROM AUTHOR]