Development of high-throughput DNA sequencing technologies has enabled scientists to generate vast amounts of genetic information that may provide a comprehensive understanding of key roles played by environmental microorganisms. Generally the microorganisms inhabit a particular niche and correlate well with environmental changes. It is accepted that the read counts obtained through metagenomic analyses correlate semi-quantitatively with the relative abundance of bacterial species. In our marine metagenomic study conducted on the Ofunato Bay, Iwate Prefecture, Japan, we observed such correlation which exists for bacterioplankton Candidatus Pelagibacter ubique, identified as the dominant bacterial species of the bay. Shotgun metagenomic analyses identified three strains of Ca. Pelagibacter in the bay, viz., dmdA-HTCC1062, dmdA-HTCC9022, and O19-dmdA, that showed a dynamic change throughout the year particularly in the 10-m depth zone. Interestingly, the total abundances of those strains that fall in the Ca. Pelagibacter genus were found to correlate well with the read counts per g seawater samples used for analyses. It is assumed that whole-genome sequence (WGS) reads for members of the metagenome would show similar trend provided that proper precautions are taken to ensure collection of representative sample from the environment.