The saccharide profiles of 5 different botanical species in 86 Italian honey samples were investigated by ¹H and ¹H-¹³C NMR spectroscopy. Nineteen saccharides were identified in the aqueous extracts, namely, fructose, glucose, gentiobiose, isomaltose, kojibiose, maltose, maltulose, melibiose, nigerose, palatinose, sucrose, turanose, erlose, isomaltotriose, kestose, maltotriose, melezitose, raffinose, and maltotetraose. PCA performed on NMR spectral regions, in particular between 4.400 and 5.700 ppm and the fructose signal at 4.050 ppm, revealed a partial sample grouping. The score contribution plots derived from PCA performed using the mean values for the buckets of the anomeric region for each floral source allowed the identification of saccharides characterizing different honeys. OPLS-DA models were further evaluated to confirm the previous findings. OPLS-DA models were also built to highlight differences between polyfloral and high mountain polyfloral honeys and between high mountain polyfloral and rhododendron honeys, both collected at high altitude; S-plots highlighted the characteristic saccharides.