Along the arid Arava, southern Israel, acacia trees (Acacia raddiana and Acacia tortilis) are considered keystone species. In this study, we investigated the ecological effects of plant species, microclimate (different areas within the tree canopies) and seasonality on the endophytic and epiphytic microbiome associated with these two tree species. 186 leaf samples were collected along different seasons throughout the year and their microbial communities were studied using the diversity of the 16S rDNA gene sequenced on the 150-PE Illumina sequencing platform.Results show that endophytic, but not epiphytic, microbiome communities were different between the two acacia species. Endophytic, but not epiphytic, microbiome was affected by temporal changes (seasons) in air temperature. Acacia canopy microclimate was also found to have a significant effect on exosphere microbiome, with A. tortilis having a higher microbial diversity than A. raddiana with significantly different community compositions in different seasons. ImportanceThe evolutionary relationships and interactions between plants and their microbiome are of high importance to the survival of plants in extreme conditions. Changes in microbiome of plants can affect plant development, growth and health. In this study, we explored the relationship between keystone desert trees and their microbiome along seasonal variation. These results shed light on the importance and uniqueness of desert phyllosphere microbiome. Although acacia trees are considered keystone species in many arid regions, to the best of our knowledge, this is the first time that microbial descriptors have been applied in these systems. This work constitutes a new approach to the assessment of these important trees and a stepping stone in the application of microbial communities as a putative marker in a changing environment.