Fourier transform infrared photoacoustic spectroscopy (FTIR-PAS) was applied to nineteen fish species in Brazil's Upper Paraná River basin to identify differences in the structural composition of their scales. To differentiate the species, a canonical discriminant analysis was used to indicate the most important absorption peaks in the mid-infrared region. Significant differences were found in the chemical composition of scales among the studied fish species, with Wilk's lambda = 5.2 × 10<sup>−6</sup>, <i>F</i><sub>(13,18,394)</sub> = 37.57, and <i>P</i> < 0.001, indicating that O-CH<sub>2</sub> wag at 1396 cm<sup>−1</sup> can be used as a biomarker of this species group. The species could be categorized into four groups according to phylogenetic similarity, suggesting that the O-CH<sub>2</sub> 1396 cm<sup>−1</sup> absorbance is related to the biological traits of each species. This procedure can also be used to complement evolutionary studies.

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