The microbial communities in air- and vacuum-packed crisp grass carp (Ctenopharyngodon idella C. et V.) fillets have not been characterized during chilled storage. High-throughput sequencing of bacterial 16S rRNA has now revealed that the bacterial community in fresh fillets is diverse and distinct from that in spoiled samples. The predominant phylum was Proteobacteria, and 66 genera were identified. In fresh fillets, the most abundant genera were Acinetobacter (53.3%), Wautersiella (6.3%), unclassified Alcaligenaceae (4.4%), Stenotrophomonas (3.8%), unclassified Enterobacteriaceae (3.8%), and Enhydrobacter (3.6%). These genera diminished during chilled storage and sometimes disappeared. At the end of storage, Aeromonas and Pseudomonas were the most abundant. Similar results were obtained by PCR–denaturing gradient gel electrophoresis. These data provide detailed insight into the evolving bacterial communities in air- and vacuum-packed crisp grass carp fillets during storage, revealing Aeromonas and Pseudomonas as major spoilage organisms. These data may be useful for improvement of crisp grass carp quality and shelf life during chilled storage.