MENTHA longifolia is one of the most vital medicinal and economic plants in Saudi Arabia. This study aimed to describe the bacterial endophytic diversity associated with the leaves and root of M. longifolia from two different locations in Al-Madinah region, Saudi Arabia, using metagenomics approach, then, correlate their deviation with the environmental stress conditions. Chemical analysis of the essential oils from M. longifolia leaves revealed the predominance of carvenone in the first location (Abyar-Ali) and pulegone in second one (Abyar-Almashi). When the irrigation water in the two locations was chemically analyzed, the results showed high content of total dissolved solids in Abyar-Ali area compared to Abyar-Almashi. On the other hand, Abyar-Almashi irrigation water had higher levels of the total organic nitrogen. Illumina MiSeq analysis of the endophytic microbiome using V3-V4 amplicons of the rRNA gene detected 114 distinct OTUs. These 114 OTUs were grouped under eight different bacterial phyla most of which belonged to Proteobacteria followed by Cyanobacteria. Within the eight phyla, all taxa were clustered into 14 class, 25 order, 41 family and 57 genera. Among the detected endophytic microbial taxa, nitrogen fixing bacteria that play a crucial role in pulegone biosynthesis, Pseudomonas, as well as Enterobacter, both excellent degrader of organic compounds were found with high abundance in Abyar-Almashi. While genus Bacillus long with other genera, either dominated or were unique to Abyar-Ali in response to the high salt stress in that location. Collectively, the previous results designate that, the dynamics in the number, type and distribution of the bacterial endophytic population between the two areas varies in response to the type of stress to which the plant is exposed.