In this study the effect of pollen source (mesquite and catclaw) on the sensory characteristics (appearance, color, aroma, taste, consistency and visible impurities), and physicochemical properties of raw propolis, and the phenolic content and biological activities of propolis extracts (PEs) was determined. The phenolic composition of PEs was determined by the total phenolic (TPC), flavone and flavonol (FFC), and flavanone and dihydroflavonol content (FDC). The individual phenolic components were analyzed by HPLC-DAD. The antioxidant activity was determined by the ferric-reducing power (FRAP) and free-radical scavenging activity (FRS). The antibacterial activity was evaluated against Gram-positive (Staphylococcus aureus and Listeria innocua) and Gram-negative (Echerichia coli and Salmonella thyphimurium) bacteria. The results showed that sensory characteristic and physicochemical properties of mesquite and catclaw propolis complied with international quality regulations. Fifteen phenolic compounds were identified, of which pinocembrin, naringenin, galangin, chrysin and quercetin were found a high concentration (> 3 mg/g). Mesquite propolis had the highest phenolic content (TFC and FDC), as well as antioxidant activity (> 2.5 mg Fe (II) equivalent/g; > 40% of DPPH radical inhibition) and antibacterial activity against Gram-positive bacterias in the order S. aureus > L. innocua (> 50% of inhibition for both bacterias at 500 µg/mL). These results indicating that pollen source affect the sensory characteristics and physicochemical properties of propolis, as well as the biological activity of their extracts.