Schinus molle is an arborescent plant that is common in North Africa. It has insecticidal and pharmaceutical activities that are assigned to some active compounds. Harmel is a cosmopolitan species extensively distributed in the world and very common in Algeria especially in the Sahara. This plant is very rich in alkaloids of the β-carbolines group of which most important are harmine. It has pharmaceutical and agrochemical virtues. Endophytic fungi were isolated from aerial part (leaves and fruits) of Peruvian peppertree (S. molle L.) Anacardiaceae and for the first time of the Harmel (Peganum harmala L.) Tetradiclidaceae.Twenty three mycotaxa were identified whose eleven isolated from S. molle and twelve isolated from the second plant. The vast majority are included in mitosporic group (Deuteromycota). The frequency of colonization or infection (FC%) at leaves of the two plants species is significant comparatively to the fruits.