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Fish tropomyosin is a latest identified fish allergen without full understanding of its biochemical characteristics from the perspective of food allergen. Accordingly, the objective of this study was to investigate the effects of species, muscle location, food processing, and refrigerated storage on fish tropomyosin and compare with main fish allergen, parvalbumin. The result of mass spectrometry analysis revealed tropomyosin as the most abundant thermally stable protein in fish muscle. Fish tropomyosin was ubiquitous among all 28 edible fish species tested, abundant in fish skeletal muscle, resistant to common food processing, and resistant to refrigerated storage up to six days. By contrast, parvalbumin content varied between fish species and was not as thermally stable as tropomyosin under autoclaving. This study demonstrates the intrinsic and processing factors affecting fish allergens and provides valuable information for the presence of major fish allergens and practical consideration of fish allergen detection.