Beneficial fungi of the genus Trichoderma occur naturally in the rhizosphere layer of the soil and are distributed worldwide. These organisms are economically important because they are used as biofertilizers and bio-factors in biofungicides, the efficacy of which is manifested in the mechanisms of antagonism: competition, mycoparasitism and antibiotics. Indigenous species of the genus Trichoderma have a more effective antagonistic and biostimulating effect. To commercialize indigenous species of the genus Trichoderma in bio-formulations, it is necessary to identify the species and to study their biodiversity and geographical distribution. Axenic fungal cultures were isolated from ten soil samples taken from the rhizosphere of Mediterranean olive trees. Six different indigenous species were identified: Trichoderma koningiopsis agg., Trichoderma atroviride, Trichoderma harzianum, Trichoderma longibrachiatum, Trichoderma paratroviride and Trichoderma sp. (unidentified species), and the most abundant were Trichoderma harzianum and Trichoderma koningiopsis agg. Classical descriptions of morphological features are not good enough for the identification of these ascomycetes, so they are complemented by modern molecular methods – DNA-barcoding of gene sequences ITS, rpb2 and tef1-α.