In order to assess the effect of pollution on marine ecosystem, we examined the plankton health assessment at 16 stations during summer season in Jinhae Bay. The organic and inorganic pollutant sources (dissolved organic carbon; DOC, chemical oxygen demand; COD and Chlorophyll a; Chl.a), including planktonic orangism such as enterobacteria Escherichia coli, heterotrophic bacteria (HB), autotrophic nano-flagellates (ANF), heterotrophic nano flagellates (HNF), ciliate and harmful algal bloom species (HABs) were used to characterize marine ecosystem health assessment. Of these, we tentatively selected those items Chl.a, HABs, HB and E. coli for plankton health index (PHI). Also, the scoring criteria for each metric were based on a statistical analysis and then, the grades are rated on four levels. As a result, the ecological assessment of these data reveals that PHI in Jinhae Bay is rated as "Good or fair" for overall conditions. The present study suggests that the PHI might be considered as one of important management tool to assess marine ecosystem health of Jinhae Bay.