Aloe dhufarensis Lavranos (Asphodelaceae) and Euphorbia larica Boiss. (Euphorbiaceae) are important medicinal plants in Oman, but little is known about the endophytic microorganisms associated with these plants and their antagonistic activities. In this study endophytic fungi and bacteria were isolated from A. dhufarensis and E. larica and their antagonistic potential against fungal pathogens attacking these plants were evaluated. The phytopathogenic fungus, Fusarium sp. from A. dhufarensis and two fungi viz., Rosellinia sanctae-cruciana and Cladosporium sp. from infected E. larica were isolated. The identification of fungi was on the basis of rDNA-ITS sequence analysis.A total of three endophytic fungi and 12 endophytic bacteria from the leaves of A. dhufarensis, and four endophytic fungi and seven bacteria from the stem and roots of E. larica were isolated. The antagonistic activity of these isolates against the phytopathogenic fungi viz. Fusarium sp. Rosellinia sanctae-cruciana and Cladosporium sp. was determined using an in vitro dual culture assay. Among them, two endophytic fungi (Sarocladium kiliense SQUCC-F2-2 and Penicillium oxalicum. strain SQUCC-F3-1) and one bacterial strain (Pseudomonas chengduensis strain SQUB1) isolated from A. dhufarensis exhibited antagonistic activity against the phytopathogenic fungi. Similarly, two endophytic fungi (Neocosmospora sp. strain SQUCC-F1-1 and Alternaria alternata strain SQUCC-F6-2) and one bacterial strain (Stenotrophomonas maltophilia strain SQUB2) recovered from E. larica showed antagonistic potential against the phytopathogenic fungi tested. These endophytic bacteria and fungi were identified based on multi-gene based phylogenetic analysis.Scanning electron microscopic observation of the hyphae of phytopathogenic fungi during interaction with the endophytes in dual culture revealed morphological abnormalities such as shriveling, pit formation, loss of turgidity, thickening of the hyphal cell walls and disintegration of the hyphae.The production of antifungal metabolites by the fungal and bacterial endophytes was invstigated. The culture filtrates of all the endophytes caused leakage of electrolytes from the mycelium of the fungal species. Among the endophytes tested, Stenotrophomonas maltophilia strain SQUB2 induced the release of more electrolytes from Fusarium sp. and Rosellinia sanctae-cruciana. Similarly, the bacterial endophyte, Pseudomonas chengduensis strain SQUB1 caused more leakage of electrolytes from Rosellinia sanctae-cruciana.GC-MS analysis of metabolites produced by the endophytes revealed the existence of various fatty acids, hydrocarbons, amines and alkanes, which have been reported to possess antimicrobial activity.This is the first study of endophytic fungi and bacteria from Aloe dhufarensis and Euphorbia larica with antagonistic activity against some phytopathogens of these plants.