The study of endophytes, of two varieties of Cannabis (Cannabis sativa L), using the root staining technique, revealed the development of different fungal structures in cannabis roots: mycelium, spores, microsclerotia, chlamydospores and perithecia. These structures belong to different species of parasitic fungi (Alternaria and Torula), and also to the pathogenic agents Fusarium and Colletotrichum. Fusarium was asymptomatically represented by macroconidia, microconidia and chlamydospores. Different stages of formation of these resistance spores were visualized on the roots of the two varieties of cannabis. The roots also showed the development of Chaetomium perithecia; structures observed in abundance on the roots of the Khedela variety. Indeed, Chaetomium generally develop on humid substrates. This study highlighted also the presence of different arbuscular mycorrhiza structures (vesicles, spores, external hyphae, arbuscules) at cannabis root level. These beneficial microorganisms can be used and exploited in future research as boosters to stimulate plant growth and vigor.