Bacterial diversity of two sponge species namely, Callyspongia and Gelliodes in the reefs of Palk Bay belonging to the class Desmospongiae has been explored in this study. From the preliminary laboratory based studies, occurrence of probable bacterial candidates producing potent bioactive compounds that are efficient as antimicrobial agents (personal communication) and biosurfactants have been established previously. Palk Bay being the highly disturbed reef environment in recent years is experiencing both natural and antropogenic stresses, mainly the domestic run offs from household and industries because of its nearshore proximity. Thus, this study attempts to report the bacterial diversity of two commonly available sponge species in the highly disturbed reefs of Palk Bay, South east coast of India through a comprehensive 16 rRNA metagenomic analysis.