Food adulteration is an important and common problem that can affect public health, safety, and the global economy. Fish is often adulterated by fraudulent activities such as mislabelling the species, substituting lower-quality or cheaper fish for higher-value species, or by adding artificial components to enhance the appearance or weight of the fish product. Here, we demonstrate an untargeted proteomics analysis method using liquid chromatography–high-resolution mass spectrometry for authenticating fish products. Our research focused on identifying peptide markers for differentiating hake and pollock, two widely consumed high-value fish that are among the most often intentionally substituted and swapped fish species. Twenty-two heat-resistant pollock-specific differentiating peptides and 17 hake-specific differentiating peptides were identified. The applicability of the method was tested using fish fillets and a popular fish product, battered fish fingers. The utility of the method for fish authenticity testing was confirmed. The proposed method can be used in food quality control laboratories. Moreover, targeted multiple reaction monitoring methods for the identified marker peptides using triple quadrupole mass spectrometry may be developed, which will facilitate and expedite the adoption of this approach by the food industry.