Both zooplankton and viruses play key roles in marine ecosystems; however, their interactions have been overlooked. Here, we introduce a case study focusing on the copepod Pseudocalanus newmani, which is one of the dominant zooplankton during winter-spring in the subarctic Pacific, and diversity and ecological roles of zooplankton were investigated. Two major viruses belonging to Picornavirales (PSNE-Pico1 and PSNE-Pico2) were detected with almost full genome sequences from P. newmani using transcriptome analysis with rRNA depletion. PSNE-Pico1 showed high viral copies and prevalence in P. newmani from late June to July, when the abundance of P. newmani decreased with increasing water temperature. On the other hand, high copy numbers and prevalence of PSNE-Pico2 were observed during spring, mainly in the early April, corresponding to the period of P. newmani population decline. Transcriptome analysis with Poly-A selection revealed large physiological changes in P. newmani with high viral loads of PSNE-Pico1. To our best knowledge, this is first study on ecological impact of viruses on marine zooplankton. Although we still need further analyses, including transmission systems of viruses to copepods and evaluation of mortality due to viruses, investigation of zooplankton-virus interactions provides a new view of marine ecosystems.