The amino acid composition of twenty-five honey samples obtained from different regions of Turkey (rhododendron and honeydew honey) was determined by a liquid chromatography-atmospheric pressure chemical ionization-mass spectrometry (LC-APCI-MS). Principal component analysis (PCA) and hierarchical cluster analysis (HCA) were used to characterize and classify the honey samples. In rhododendron honeys, major amino acids were detected as aspartic acid, lysine, and arginine, for honeydew honeys, lysine, arginine, and histidine were found, following the proline. Five principal components (PCs) and four main clusters were obtained from the chemometric analysis that classifies the samples. Five PCs were detected to be explanatory of more than 79% of the total variance in the data matrix. It can be concluded that free amino acids are good indicators for determination of botanical origins and chemometric studies are highly useful for honey characterization.