Internal colonizers of bacteria were isolated from gut after partial surface sterilization using UV irradiation and the subsequent dispersal treatment. Genomic DNA extraction from each isolate was performed with a FTA TM card (Whatman, UK), and then PCR-amplified, targeting 16S rDNA fragments with universal primer pairs. The PCR products were purified and then sequenced to identify a series of bacterial strains collected during this study. Most of the gut floras were members of the Aeromonas group commonly distributed in aquatic habitats, whilst others were identified as Paucibacter and Acidovorax, both may degrade native and manmade toxic materials such as cyanotoxin and dioxin, respectively. These normal floras of invertebrates inhabiting slow sand filters contribute not only to purify water but may decompose unfavorable toxic substances, presumably reducing potential health risks during drinking water production.