Mangrove forests are highly productive ecosystems widespread in tropical and subtropical coastlines, with a coverage of 75% of the world’s tropical shorelines. Mangrove plants developed specific physiological and morphological adaptation to thrive in such unique environments. Together with plant adaptations, mangroves develop a tight partnership with microorganisms, mainly bacteria and fungi, that form the so-called mangrove-microbiome. Plant-associated microorganisms are generally recruited by the root system (root tissues and rhizosphere) and the colonization process starts with the release of root-related exudates detected by the surrounding edaphic microorganisms that are attracted in the rhizosphere zone. Then, root surface selects those microorganisms that can enter the tissues as endophytes. The microorganisms recruited belowground can migrate through the plant tissues by using the plant vessels and may colonize the aboveground compartments of the plant. Here, I aimed to evaluate the environmental origin and compartmentalization of the mangrove microbiome. To do this, I sampled bulk sediments, sea water, and mangrove plant compartments (root rhizosphere and endosphere, pneumatophores, shoot, leaves, flowers and propagules) of 20 gray mangrove trees (Avicennia marina L.) across two sites on the Red Sea coast of the King Abdullah University of Science and Technology (KAUST), Saudi Arabia. By high-throughput sequencing of the bacterial 16S rRNA gene, I showed that the bacterial assembly in A. marina plant compartments follows a clear niche partition process in which bacterial communities are actively recruited from the surrounding ecosystem (sediment and sea water) by the root system, and further distributed across the different plant organ and compartments. Moreover, the composition of microbiome detected had many similitudes with others previously described around the world, suggesting that certain bacteria represent a mangrove “core microbiome”. The conservation of microbiome composition, mainly driven by environmental and host selection, that beneficial bacteria provide to the plant and contribute to its growth and fitness by several mechanisms. Thus, the characterization and identification of mangrove microbiome can meliorate our knowledge regarding plant–microbe interactions, as well as put the bases for the development of Nature-based Solution (NBS) to enhance reforestation and rehabilitation of mangrove ecosystems