Rapid and simple analytical methods for viable microorganism detection in ballast water are required to evaluate the efficiency of ballast water treatment system. During the course of systematic investigation of the cytotoxicity and apoptosis assays, it was found that the adenosine triphosphate (ATP) and luminescence based cell viability assay, in other word, an ATP assay was the most sensitive and applicable to ballast water management (BWM). The assay was applied to cultured microalgae samples, and it could detect the existence of 5 viable cells in 100 μl. Comparably low luminescent values were detected in two cultured diatom species than in cultured dinoflagellates. This result might be caused by the small cell volume in diatom species. Following a regression model between ATP concentration and cell volume, an ATP guideline (876 – 109246 relative luminescence units: RLU) was developed for the evaluation of treated ballast water. ATP assay was also applied to the evaluation of ballast water treatment system (BWTS). The luminescence value which obtained from the ATP assay also showed a good correlation with the presence of living natural plankton cells with comparably low luminescence values than the cultured species. The low ATP concentration in natural plankton cells may reflect a decline in their biological activity because of extended exposure to dark conditions. ATP assay could be a suitable method for the monitoring of ballast water management compliance even though the results of this study need further validation.