The chemical characterization as well as the assessment of geographical origin of propolis from several areas of the Provincia de San Juan (Argentina) is reported. Chemical characterization of propolis was performed by measuring total phenolic (TP), total flavonoids (FL), free radical scavenging capacity (DPPH bleaching), and metal content in samples of six different districts. Methanolic propolis extracts (MEP) showed TP ranging from 25.7 to 39.3 g of gallic acid equivalents per 100 g of MEP, whereas flavonoids ranged from 6.6 to 13.3 g of quercetin equivalents per 100 g of MEP. Six main flavonoids were isolated and identified from the propolis samples, comprising the flavanones 7-hydroxy-8-methoxyflavanone (1), pinocembrin (2), and pinobanksin (3), the flavones chrysin (4) and tectochrysin (5), and the flavonol galangin (6). Compounds 1-6 were quantified by HPLC-PDA. Free radical scavenging activity, measured as percent DPPH bleaching, ranged from 46.6 to 89.5 at 10 mug/mL. Moreover, propolis samples presented high contents of Ca, K, Fe, Na, and Mg, but low amounts of Mn and Zn. Linear discriminant analysis affords eight descriptors, galangin, pinocembrin, pinobanksin, chrysin, tectochrysin, DPPH, K, and Na, allowing a clear distinction with 100% accuracy among different origins within the Provincia de San Juan. A direct relationship of DPPH free radical scavenging activity with TP or with compounds 1-6 was not found, showing the need of further evaluation on the origin of free radical activity in propolis samples.