Chemical fertilizers have been utilized to provide nutrients to plants and resulted in rapid increase of agricultural productivity, which is important to achieve the growing world population’s demand for food. However, chemical fertilizers can be harmful, with negative effects on the environmental ecology and human health. Therefore, biofertilizers are considered as the best substitute for chemical fertilizers for enhancing the growth of host plants. In this study, mangrove-associated microbes collected from soils were analyzed and used to develop biofertilizer. The first objective of this study was to identify a wide range of microbial species and function of genes from three soil samples collected at the freshwater riverine mangrove at Sungai Lukut, Negeri Sembilan, Malaysia by using metagenomic Whole Genome Shotgun Sequencing (mWGS). The second objective was to isolate and identify bacterial species grown on selective media which are nitrogen fixing bacteria, potassium solubilizing bacteria and phosphorus solubilizing bacteria by using PCR and sequencing of the 16s rRNA gene. The last objective was to determine the selected bacterial species that can affect duckweed plants in terms of growth rate and protein contents. Results from mWGS analysis show different distribution of bacteria of the genera Bradyrhizobium, Methyloceanibacter and Desulfobacteaceae were detected in soil samples collected from the three locations. For culture-depending technique, bacterial species that grew on selective media were identified as Acinetobacter radioresistens, Brachybacterium paraconglomeratum and Enterobacter cloacae which are screened as nitrogen-fixing bacteria, Klebsiella quasipneumoniae, Bacillus tropicus, and Paenibacillus pasadenensis screened as potassium solubilizing bacteria, and Bacillus cereus and Bacillus thuringiensis screened as phosphate solubilizing bacteria. Next, three sets of biofertilizers that include Set A containing A. radioresistens, K. quasipneumonia and B. cereus, Set B that contains B. paraconglomeratum, B. cereus and B. tropicus, and Set C containing E. cloacae, P. pasadenensis and B. thuringiensis with 106 cfu/g were formulated by mixing each set of bacterial species with commercial compost. The results showed that Set C is the best biofertilizer set compared to Set A and Set B as it can increase the content of nitrogen, phosphorus and potassium in the soil and increase the growth and protein of the duckweed plants. This indicates that biofertilizers formulated with mangrove-associated bacteria could enhance the growth of duckweed as well as its protein content.