In this study, the diversity of endophytic and epiphytic fungi communities was evaluated and compared from healthy, symptomless and green leaves of the medicinal plant Ziziphus lotus (wild jujube) growing in Northern Algeria. Culture-based methods were used to isolate the endophytes and epiphytes. Morphological and molecular analyses were applied for identification of the fungi taxa. Both communities of the phylloplane of Ziziphus lotus differed in size and composition. Out of all 52 species, 19 were identified as epiphytic fungi and 45 as endophytes with 12 species shared by the two communities (Aspergillus costaricaensis, A. tubingensis, Aureobasidium sp., Cladosporium asperlatum, C. halotolerans, C. limoniforme, Penicillium chrysogenum, P. desertorum, P. flavigenum, P. momoii, Stemphylium sp. and Trichothecium crotonigenum). The two communities were found to be moderately similar (Sørensen similarity index = 0.37). Higher diversity values were found in endophytic community compared to epiphytic community: Shannon's diversity index H' (3.29 vs 1.83), Simpson diversity index C' (0.94 vs 0.74), species richness (3.06 vs 0.46) and species evenness (0.86 vs 0.62). Additionally, the correlation matrix was generated for the identification of possible interactions between different fungi.