The characterization of amaranth seeds (Amaranthus spp.) was developed for Amaranthus hypochondriacus, Amaranthus cruentus, and Amaranthus dubius. The elemental concentrations were determined by inductively coupled plasma optic atomic spectroscopy. Pattern recognition methods were used for the characterization of seed samples: nonsupervised methods included principal components analysis and cluster analysis; supervised methods were linear discriminant analysis and partial least squares discriminant analysis (PLS-DA). Informed are the concentrations of the following elements: Ag, Al, Ba, Ca, Co, Cr, Cu, Fe, K, La, Li, Mg, Mn, Mo, Na, Ni, P, S, Sr, V, Zn, and Zr. The lowest mineral content was found in A. hypochondriacus, and the highest one was found in A. dubius. For the classification, selected variables for all multivariate methods were Ba, Cr, Li, Mn, Ni, S, and Sr. Nonsupervised methods allowed us to distinguish between the three species of amaranth; however, PLS-DA supervised methods showed the best prediction ability.