MicroRNAs (miRNAs) are non-coding RNA molecules, very short in size approximately 18–22 nucleotide long. The miRNAs play a very significant role in the growth and development of plants. They are also reported to be stress responsive and thereby help in maintaining homeostasis inside plants system. Mangrove is ecologically as well as economically very important an ecosystem, growing in the tropical and sub-tropical estuaries. But various natural phenomena such as global warming, sea-level rise, and salinity rise have proven to be catastrophic for this vegetation and some species are getting depleted at an alarming level. In that context, it would be of immense importance, to study the role of these miRNAs in regulating homeostasis in the mangroves. In this present study, we have identified four stress-induced miRNAs – ra-miR11103, ra-miR1134, ra-miR166h, and ra-miR5206 from a profusely growing mangrove species Rhizophora apiculata. The predicted target sequences, all of these found out majorly to be proteins and enzymes responsible for abiotic stress tolerance in plants, except for ra-miR1134 which included both biotic as well as abiotic. This result definitely points toward the regulatory role of the miRNAs toward maintaining cellular homeostasis. Experimental validation and molecular characterization of these miRNAs might provide important insights about their role in combating biotic and abiotic stress, which when compared with the plants which are on the verge of extinction might provide information useful for understanding the exact reason of their distressed nature, which, in turn, would be immensely helpful for planning the proper conservation of those plant species.