Diurnal vertical migration of zooplankton plays a large role in the active transport of organic matter to the deep ocean, as part of the biological pump. The vertical distribution of the zooplankton over a diel cycle is fundamental to unveil the active migration population and their roles in biological pump. In this study, we collected mesozooplankton at C6 and C9 stations in Taiwan Strait, China. Samples were collected every 6 h over a diel cycle with three 200µm-mesh plankton nets. The three replicate net tows were used for microscopic, DNA and RNA analysis, respectively. Both 18S rDNA and rRNA of each sample were amplified by eukaryotes-universal primers embracing V4 region.