Two kinds of fish-derived natural antimicrobial substances, protamine and catfish ( Clarias fuscus ) epidermal mucus extract (CEME), were evaluated for their effect on the quality of grass carp fillets. Fillets were atmosphere packaged in cast polypropylene bags and were stored at 4°C in a low-temperature incubator without light. Solutions (0.5%, wt/vol) of CEME and protamine were used for dip pretreatment, respectively. Bacteriological (aerobic plate count, Shewanella putrefaciens , Pseudomonas fluorescens ) and physicochemical (pH, total volatile basic nitrogen, K value, surface color, texture profiles, water distribution) parameters and volatile odor compounds were measured on days 0, 3, 6, 9, 12, and 15. The results indicated that CEME and protamine could improve all bacteriological and physicochemical indexes, except water distribution within muscle. In comparison, CEME had a more inhibitory effect, as determined by the aerobic plate count, and was more effective in inhibiting the growth of P. fluorescens ; however, protamine was more effective in preventing the production of sulfur-organic (H2S) group substances. Protamine was more effective in inhibiting the growth of S. putrefaciens . This research suggests that protamine and CEME have the potential to improve the quality and extend the shelf life of grass carp fillets.