Accurate authentication of related species is necessary to prevent the illegal replacement of species of higher quality and/or price with lower-quality, less expensive species. Atlantic salmon (Salmo salar), an expensive and valuable species, can be intentionally substituted with rainbow trout (Oncorhynchus mykiss). Using the technique of capillary zone electrophoresis (CZE), the identification of raw species was based on the analysis of muscle sarcoplasmic (water-soluble) proteins, while for canned species identification was based on muscle proteins solubilized with urea and sodium dodecyl sulfate (SDS). Either water or urea-SDS extracted proteins gave reproducible and distinct electrophoretic patterns of proteins for both species independent of storage conditions. Although data analysis indicated changes in protein profiles for both species during storage, species identification was still possible. In addition, quality determination during refrigerated and frozen storage involved the use of two freshness indexes: K value (the relationship between inosine monophosphate, inosine, and hypoxantine) and pH. A linear correlation was found between changes in electrophoretic patterns and K values for refrigerated salmon species. Trout kept in storage for six days reached a constant K value higher than the maximum limit for a product of good quality, preventing determination of any correlation with electrophoretic pattern. The protein profiles obtained by CZE during long storage revealed their potential for monitoring both differences between fish species and changes in quality during refrigerated, frozen, and canned storage of the species under study.