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Near infrared (NIR) spectroscopic investigations of whole fish and fish fillets with a miniaturised, hand-held instrument were performed to demonstrate the feasibility of discriminating high-quality, expensive from lower-quality, less expensive, substitutes and responding to the increasing concerns regarding fraud and deception in seafood marketing. Generally, such problems can occur due to the mislabelling of products in the harvesting and processing system or species substitution at the restaurant level. To test the possibility of distinguishing superior from lower quality fish species, NIR spectra were measured in diffuse reflection from the skin and meat of the investigated fish. Subsequently, the spectra were evaluated by principal component analysis and further classified by soft independent modelling of class analogies. In the present communication, the results obtained with respect to the authentication of two different species of mullet, cod and trout, respectively, will be discussed in some detail.