In the present study, with the aim of understanding the effects of the gigantic earthquake and its resulting tsunami in Tohoku area on marine biodiversity and ecosystem, we develop a meta-genomic method of observing a variety of marine microorganisms at once and its practical application to environmental monitoring. Utilizing the methods developed, we make assessment of marine environments by comparing the diversity of microorganisms in spots along the sea coasts between Tohoku area and other areas. The outcome of the present study is expected to make contributions to deeper understanding of marine ecosystem of microorganisms.