Identification of specific mycotoxins p. Fusarium contained in infected winter wheat seeds can be achieved by visually recognizing their distinctive phenotypic species. The visual identification (ID) of species is subjective and usually requires significant taxonomic knowledge. Methods for the determination of various types of mycotoxins of the p. Fusarium are laborious and require the use of chemical invasive research methods. In this research, we investigate the possibility of using Raman spectroscopy (RS) as a tag-free, non-invasive and non-destructive analytical method for the rapid and accurate identification of p. Fusarium. Varieties of the r. Fusarium can produce mycotoxins that directly affect the DNA, RNA and chemical structure of infected seeds. Analysis of spectra by RS methods and chemometric analysis allows the identification of healthy, infected and contaminated seeds of winter wheat with varieties of mycotoxins p. Fusarium. Raman seed analysis provides accurate identification of p. Fusarium in 96% of samples. In addition, we present data on the identification of carbohydrates, proteins, fiber and other nutrients contaminated with p. Fusarium seeds obtained using spectroscopic signatures. These results demonstrate that RS enables rapid, accurate and non-invasive screening of seed phytosanitary status.