Physicochemical changes of muscle from croaker, lizardfish, threadfin bream and bigeye snapper during storage at −18 °C were investigated for up to 24 weeks. Ca2+–ATPase activity decreased, whereas Mg2+–EGTA–ATPase activity increased throughout the storage. However, no marked changes in Mg2+–Ca2+–ATPase and Mg2+–ATPase activities were observed. Among all species tested, lizardfish muscle was most susceptible to those changes. Disulfide bond formation with the concomitant decrease in sulfhydryl group was found in all species. However, croaker and lizardfish contained higher disulfide bonds as storage time increased, compared to other species. Surface hydrophobicity increased in all species with the sharp reduction observed in lizardfish after 12 weeks. For all species, α-glucosidase and β-N-acetyl-glucosaminidase activities increased in association with the increased expressible drip. Therefore, extended frozen storage caused the denaturation of protein as well as the cell disruption in all species, but the degree of changes was dependent upon species.