Environmental effects are determining factors for the activity of the antioxidant compounds and fruit form. Samples of M. communis, originating from two biogeographically different zones in Morocco, were collected to study the variation in fruit size, fruit extract yield, and content of antioxidant compounds and activity of fruit extract and to examine its association with provenance environmental effect. Analysis of the results shows significant effect of provenance and environmental factors of several traits studied except anthocyanin compounds and IC50. The high content of polyphenols, flavonoids, and extract yield are associated with less watered and warm sites, and with low altitudes. Also, selection for one of the traits of fruit size and/or extract yield could favor selection for one of the phytochemicals. The aggregation of the populations studied using traits studied identify three main groups. These results are interesting for the selection of elite natural populations in favor of programs to promote this species for applications in the food, therapeutic, pharmaceutical and cosmetic fields.