Mangroves in arid environments represent unique ecological niches that support a diverse range of microorganisms. Endophytic bacteria residing within host plants play a crucial role in promoting plant growth by enhancing pathogen resistance and alleviating environmental stress. Identifying novel stress-tolerant strains, specific to arid environments, is essential for expanding the repertoire of plant growth-promoting bacteria (PGPB). In this study, we investigated the saline tolerance of the endophytic bacterium strain E1, previously isolated from the root of Avicenna marina (grey mangrove). Whole-genome sequence (WGS), phylogenetics and average nucleotide identity (ANI) analysis were performed. The strain exhibited high salinity tolerance, growing in conditions up to 11% NaCl, and was phylogenetically closely related to Bacillus cereus. Genome analysis revealed multiple PGP-related genes, including those involved in nitrogen fixation, phosphate and potassium solubilization, and iron siderophore transport. Additionally, genes associated with detoxification, hormone biosynthesis (Including Indole-3-Acetic acid and cytokinin), salt and heat stress tolerance, as well as volatile compound production, were identified. A greenhouse assay with tomato plants was conducted to assess the ability of strain E1 to alleviate saline stress (50, 100, and 150 mM NaCl) and its impact on spectral indices, antioxidant enzymes, and electrolyte leakage (EL). Inoculation with strain E1 significantly enhanced all measured growth parameters, including shoot and root length and weight (both fresh and dry) as well as leaf area. These improvements were reflected in elevated spectral indices, increased antioxidant enzymes, improved cell stability, and reduced EL compared to control and NaCl-treated plants. These findings highlight Bacillus cereus strain E1 as a promising, stress-tolerant endophyte for arid agriculture, capable of promoting tomato growth through multiple mechanisms under challenging environmental conditions.