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Mulberry (Morus spp.) has always been a favorite plant of gardners, farmers and researchers because of its edible fruits, medicinal properties and timber. We have investigated the morphological, physiological and chemical variabilities of white (Morus alba), red (Morus rubra) and black (Morus nigra) mulberry genotypes grown in four regions of Iran. Among the genotypes assessed, fresh fruit weight varied between 3.2 and 87.9 g, total chlorophyll ranged from 4.3 to 13.4 mg/g fresh weight and vitamin C content ranged from 5.5 to 64 mg per 100 g. The highest and lowest antioxidant activity was 275 and 1575 mg ascorbic acid equivalent (AAE) 100 g−1 fresh weight, respectively. The population analysis indicated that the Gorgan population, in terms of morphological and physiological traits, and Shahrood population, in terms of chemical traits, had the highest coefficient of variation. Correlation analysis showed that fruit size and taste were positively correlated with foliar traits and that phenolic content was positively correlated with both antioxidant activity and total soluble solids (TSS). Of the indices assessed, the Berger–Parker index was the most valuable because it was able to identify significant differences between populations in terms of the studied traits. The results of this study confirm that Iran is one of the mulberry phenotypic and biochemical diversity areas and provide information of possible use for the development, conservation and selection of parents for cross-combinations in breeding programs.