This paper proposes a method based on near-infrared hyperspectral imaging for discriminating between terrestrial and fish species in animal protein by-products used in livestock feed. Four algorithms (Mahalanobis distance, Kennard-Stone, spatial interpolation, and binning) were compared in order to select an appropriate subset of pixels for further partial least squares discriminant analysis (PLS-DA). The method was applied to a set of 50 terrestrial and 40 fish meals analyzed in the 1000-1700 nm range. Models were then tested using an external validation set comprising 45 samples (25 fish and 20 terrestrial). The PLS-DA models obtained using the four subset-selection algorithms yielded a classification accuracy of 99.80%, 99.79%, 99.85%, and 99.61%, respectively. The results represent a first step for the analysis of mixtures of species and suggest that NIR-CI, providing valuable information on the origin of animal components in processed animal proteins, is a promising method that could be used as part of the EU feed control program aimed at eradicating and preventing bovine spongiform encephalopathy (BSE) and related diseases.