In this study, the effect of species composition on the stability and reproductivity of small-scale microcosm system was investigated. Small-scale microcosm system in this study was gnotobiotic type, which consisted of micro animals as predator, algae as producer and bacteria as decomposer. Three species of protozoa and three species of metazoa as predator, seven species of algae as producer and four species of bacteria as decomposer were employed. With these microorganisms, twenty-four sorts of species composition were made to investigate their effect on stability and reproductivity of microcosm system. As a result, some systems showed very high stability and reproductivity while some did not. And it was suggested that this high stable and reproductive microcosm system can be used as one of tools to assess the effect of genetically engineered microorganisms, micro pollutant and so forth on ecosystem level, because has enough capability to be applied as standard.