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Crisp grass carp is a type of grass carp (Ctenopharyngodon idella) that has been fed faba beans. Flesh quality and expression of muscle quality-related genes in muscle of grass carp were evaluated. Compared with ordinary grass carp, 1901 differentially expressed genes (DEGs) were up-regulated and 1628 DEGs were down-regulated in crisp grass carp. The GO analysis results showed that the DEGs were enriched in ribosomes and proteins. Kyoto Encyclopaedia of genes and genomes (KEGG) pathway analysis results showed that amino acid metabolism was closely related to meat quality. COX3, ACADS, ACAT1, ECHS1, EHHADH, HADHAA, HADH, HMGCL, MCCC1 and MCCC2 were the top 10 hub genes most closely associated with other nodes and showed a strong positive correlation. Hardness was positively correlated with the COX3, ECHS1, ACADS, ACAT1, HADHA, HADH, HMGCL and MCCC1. These results have been demonstrated to play important roles in clarifying the molecular mechanism of muscle firmness increase in crisp grass carp.