This study was conducted to identify the fungi and bacteria associated with fish waste decomposition. The rotten fish was ground and setup in blue tank approximately 15 kg for each tank closed with net and left in the tank for 30 days to decompose. Physicochemical parameters including pH, temperature, moisture content and carbon to nitrogen (C:N) ratio were monitored throughout the process. Culture-dependent methods were used to identify the diversity of bacteria and fungi in this study. Fungi were isolated using eight different media with various compositions; potato dextrose agar, Rose Bengal agar, peptone water agar, Saboroud agar, yeast extract agar, oatmeal agar, malt extract agar and leachate medium agar while bacteria were isolated on yeast extract agar, diluted nutrient agar, leachate agar and tryptone agar. Fungal isolates were extracted using CTAB followed by 18S rRNA amplification using primers set FF390/FR1 meanwhile, PCR amplification of the 16S rRNA gene using primer sets 27F/1492R was performed directly from the bacterial colonies. Results from DNA sequencing were analyzed using BLASTn, and phylogenetic tree were constructed using ARB software. During the decomposition process, temperature of waste was in the range between 20-50°C, pH 6-8, moisture content started at 80% and reduced to 50% and C:N ratio 3-7. A total of 41 fungal isolates and 25 bacterial isolates were identified based on 18S and 16S rRNA gene respectively. For fungal isolates, the Ascomycota (91% of all sequences recovered) were the dominant phyla followed by Basidiomycota (9%). The 41 randomly isolated fungi were belonged to 22 OTUs of the genus Exophiala, Penicillium, Aspergillus, Monascus, Parengyodontium, Fusarium, Trichoderma, Chaetomium, Hypoxylon, Candida, Curvularia, Cladosporium, Paraconiothyrium, Cymatoderma and Trichosporon. From 16S gene rRNA identification and comparison, the 24 bacteria belonged to Pseudomonas, Bacillus, Enterobacter, Klebsiella, Stenotrophomonas, Alcaligenes, Acinetobacter, Streptomyces, Micrococcus, Brevundimonas, and Proteus. The utilization of different agar medium increase the possibility of isolating the diverse of fungal and bacterial community involved in fish waste decomposition.