This study reports the combination of multivariate techniques and pollen count analysis to classify honey samples accordingly to botanical sources, in samples from Uruguay. Honey samples from different botanical origins, namely
Eucalyptus
spp. (n = 10),
Lotus
spp. (n = 12),
Salix
spp. (n = 5), "mil flores" (
Myrtaceae
spp.) (n = 12) and coronilla (
Scutia buxifolia
Reissek) (n = 10) were analysed using Melissopalynology (pollen identification). Principal component analysis (PCA) and linear discriminant analysis (LDA) were used to classify the honey samples accordingly to their botanical origin based on a pollen count. Honey samples of higher percentage (> 70%) of
Eucalyptus,
Lotus and
Scutia pollen were 100% correctly classified, whilst samples from
Myrtaceae
spp. and
Salix were 80 and 66% correctly classified, respectively. The use of PCA and LDA combined with pollen identification proved useful in characterizing honey samples from different botanical origins.