Honeys from different regions of Algeria were analyzed to determine their pollen characteristics and physicochemical properties (humidity, pH, electrical conductivity, diastase content, color, phenols, flavonoids and antioxidant activity). The antioxidant activity was investigated using the free radical scavenging and Ferric reducing/antioxidant power assays. The melissopalynological analysis revealed 129 pollen types from 53 botanical families. The pollen types found as dominant were Coriandrum, Bupleurum, Brassica napus type, Hedysarum coronarium, Ceratonia siliqua, Eucalyptus, Peganum harmala, Ziziphus lotus and Tamarix. Principal component analysis and cluster analysis were used to analyze significant relationships between the physicochemical variables and the botanical origin of the honeys and establish groupings based on the similarities of their physicochemical and antioxidant properties. The results showed that Ceratonia siliqua, Eucalyptus, Arbutus and honeydew honeys had a higher antioxidant contribution and higher phenolic and flavonoid contents than the rest of the honeys. In addition, the contributions of Mediterranean vegetation such as Myrtus and Phyllirea angustifolia were significant in this honey group. This paper demonstrates the diverse botanical variability for honey production in Algeria. However, there is a gap in its characterization based on its botanical origin. Therefore, these studies contribute positively to the needs of the beekeeping sector and the commercial valorization of the country’s honey.