[Background] Virioplankton is one of the most important components of microbial communities. The study on the temporal and spatial distribution of the virioplankton contributes to the protection and development of local microbial resources. [Objective] Virioplankton and planktonic bacteria of water samples were counted, aiming to investigate the virioplankton distribution in the Napahai plateau wetland. [Methods] Water samples from seven sites were obtained in December 2013 and September 2014. Virioplankton and planktonic bacteria abundance were determined using flow cytometry. Here we reported on virioplankton relationships with environmental factors, such as bacterial abundance, chlorophyll a concentration and other environmental factors. [Results] Virioplankton and planktonic bacteria abundance in rainy season was higher than that of in dry season at the seasonal distribution. Virioplankton abundance in dry season was influenced by bacteria abundance and chlorophyll a concentration; whereas virioplankton abundance in the rainy season was influenced by pH and temperature. [Conclusion] We found high virioplankton and planktonic bacteria abundance values. Virioplankton abundance was correlated with bacterioplankton abundance and chlorophyll a concentration in different seasons and sampling points. The phage, rather than the algal or phytoplankton viruses, was the dominant population in dry season of the Napahai plateau wetland.