Natural products played a key role in drug discovery. More than 50% of currently available FDA-approved drugs are either directly or indirectly derived from natural origin. However, novel therapeutic agents such as antimicrobial and anticancer drugs are continuously in demand. Marine environment is the most recent promising target for discovering new bioactive natural products. Sponges are sessile marine invertebrates which are known to be a rich source of structurally unique and chemically diverse secondary metabolites with potent biological activities. These metabolites have been frequently hypothesized to be of bacterial origin. More than 99 % of bacteria are challenging to be cultured under the frequently laboratory conditions so culture independent techniques such as metagenomics and metatranscriptomics have been used as effective tools to study the sponges associated bacterial community. These techniques also provide a mean of discovering new bioactive metabolites from the associated communities with the help of many computational and bioinformatics tools.