Sponges are host organisms for various symbiotic microorganisms such as archaea, bacteria, cyanobacteria and microalgae. Sponges are also sources of a wide variety of useful natural products like cytotoxins, antifouling agents, antibiotics, and anti-inflammatory and antiviral compounds. Symbiotic microorganisms in sponges can be sources of various natural products, because metabolites previously ascribed to sponges have recently been demonstrated to be biosynthesized by symbionts. If a symbiotic microorganism from which some natural products are derived can be cultured, the microorganism could be used in a mass production of the bioactive compounds. We summarize recent research on isolation and cultivation of sponge-symbiotic microorganisms and the symbiotic relationship.