Microflora of fish intestines appear to vary with the complexity of the fish digestive system. The genera present in the gut generally seem to be those from the environment or diet which can survive and multiply in the intestinal tract. The main aim of the work is to identify the organism present in the gut of fish through ribotyping technique. To start up with the procedure first standardized the ribotyping technique. For standardization of the procedure a gram+ve(Bacillus) and a gram-ve (E.coli) was used. Genomic DNA was successfully isolated from both organisms. Hot shot method was performed. PCR method was standardized. As the procedure standardized the microflora present in the fish gut was successfully isolated by serial dilution. Sixteen morphologically different colonies were got. DNA was isolated using hotshot method. Extracted DNA was subjected to PCR amplification. Four samples showed strong bands and send for sequencing.