In this study we have isolated and characterized yeasts from the soil, leaves and fruits of the indigenous Moroccan Argan tree (Argania spinosa) in two locations: the coastal city of Essaouira and a drier, more stressed environment in Taroudant city. Factorial and classification analyses of the metabolic profiles showed that the yeasts from the soil and those from the fruit seemed to form distinctive groups while those from the leaves were common to the two groups. Associating the profiles with yeast species, the soil isolates seemed to be dominated by profiles associated with basidiomycetous yeasts (Bullera variabilis, association to Filobasidium capsuligenum, and Rhodotorula glutinis) while those of the fruits were associated with ascomycetous yeasts (Pichia angusta and Zygoascus hellenicus). Most profile groups were shared between the leaves and one of the other biotopes owing to the semi-deciduous character of the Argan leaves that dominate in the rhizospheric soil and to the fibrous and low flesh fruits of Argan. Although most metabolic profile groups were represented in both sampling locations, certain groups were encountered only in Taroudant samples among which a group of four yeasts that grew at 44 °C. The Taroudant samples also presented the two most osmo-tolerant yeasts capable of growing at 15% NaCl and 125% sucrose. Some of the yeast strains showed very promising activities of polygalacturonase (0.40 units/g protein) without any pectinesterase activity while others strongly inhibited the gray rot mould Botrytis cinerea, and could be good candidates for the post-harvest control of this mould on fruits.