Abstract: The green honey food product from honeybee is produced in the forest's subsurface region on Banggi Island, Because of its uniqueness, the product attracts a great market price. Naturally the honey doesn't acquire microorganisms due to strong chemical property and dormant nature. Major causes of microbial contamination are probable to include pollen, the digestive tracts of honeybees, sources that are extremely difficult to control include earth, air, dust, and nectar. This study was carried out to determine the microbial diversity of green honey using amplicon sequencing method, we targeted 16S rRNA V3-V4 region for bacterial species and ITS1 region for fungal diversity. Result revolved that; Bacteria include the largest number of identified taxa (256) and read (136856400), total of (118) different bacteria species identified and validated with seven distinct phyla, namely protobacteria, Firmicutes, Actinobacteriota, Bacteriodata, fusobacteriota, chloroflexota, and some unclassified phylum. Among other identified species only 11 bacterial species relative abundance is higher than one percent. Fungi is the second largest with 08 taxa identified and number of read (16217100). Six different species of fungi and only two species of yeast were identified, all the identified species were belong to two different phyla Ascomycota and Basidiomycota. Among other identified genera genus Zygosaccharomyces have relative abundance (99%) as compared to other species identified, it reflects the very high abundance of Zygosaccharomyces in green honey sample.