Mangroves are important coastal wetlands along tropical and subtropical regions. Pneumatophore, a kind of aerial root, is among the prominent components of a mangrove ecosystem, which provides microhabitats for a range of prokaryotic (bacteria and cyanobacteria) microbial assemblages, whose role in the maintenance of mangrove ecology often remains neglected. Very few studies are available on pneumatophore-associated prokaryotic microorganisms (PAPMs). The majority of them are related to the microscopic identification of cyanobacteria, with very limited research on the bacterial population, even though they demand more attention. Also, very scarce information is available on biotic and abiotic factors shaping the PAPMs. The objective of this review is to highlight the structural and functional importance of prokaryotic organisms associated with pneumatophores. This review begins with a brief introduction of what mangrove pneumatophores are, then focuses on the PAPMs, accentuating the breadth and depth of information gained from previous research. We further discuss how a combination of a traditional cultivable approach and a newly developed omics approach can be efficaciously employed to untangle PAPMs. This review provides updated information on PAPMs, which will intensify the visibility and necessity of pneumatophore-associated microbial community research.