With the objective of evaluating the utility of the amino acid profile in the characterization of honey samples, 39 honey samples of two different harvests from a particular production zone in Córdoba, Argentina, were analyzed. Multivariate statistical techniques, such as principal component analysis (PCA), cluster analysis (CA), and multiple correspondence analysis (MCA), were applied to verify the correlation among the amino acid profiles, pollen percentages, and different harvests. PCA, CA, and MCA demonstrate the presence of differences of amino acid profiles between samples of the two harvests, such differences being mainly due to differences in pollen availability. Variation of the flora surrounding the apiary due to agricultural practices makes the analysis of amino acid profile typical for those cases with stabilized flora.