The microbiome present in mangrove ecosystems plays a vital role in the sustainability and well-being of mangroves, especially as our planet continues to change. Nevertheless, the precise elements that affect the biogeographical distribution of these microorganisms within mangrove environments remain largely unclear. Mangrove ecosystems offer significant ecological advantages and services, such as carbon sequestration and coastal protection; however, they face considerable human-induced threats. The microorganisms found in mangrove sediments are crucial to this ecosystem, contributing significantly to its microbial diversity and productivity, which in turn supports various medicinal properties derived from both plants and their associated microbes. Recognizing this interconnection necessitates a shift from merely descriptive studies of microbial taxonomy and from its medicinal values, secondary metabolites, and its derivatives. However, in the last few decades, some natural and man-made factors have been responsible for reducing the mangrove forest and associated microbial diversity. The current study focused on the microbial diversity associated with microbes, showing various medicinal importance that need to be conserved for controlling carbon storage, maintaining the aquatic flora and fauna, and ultimately protecting the coastline.