Predator and prey diversity are commonly found to be positively associated. Several verbal arguments are proposed to explain such association, but they receive limited supports. The mechanisms underlying such positive association remain unclear. We believe that viewing this puzzle through the lens of community assembly processes could be informative because community assembly processes determine the diversity of a community. We thus hypothesize that the predator (prey) diversity influences community assembly processes acting on the prey (predator) community, which then determines the prey (predator) diversity. To test this hypothesis, we calculated the Shannon diversity of heterotrophic nano-flagellates (HNF; predator) and bacteria (prey) collected in the southern East China Sea. We also inferred the community assembly processes from their phylogeny. We found that HNF diversity was positively associated with the community assembly processes acting on bacteria community, which was then positively related to bacterial diversity. In contrast, bacterial diversity was not related to HNF’s community assembly processes. These results suggests that predators impose certain selection forces on prey community, so that predator and prey diversity are related. This study not only offers an explanation but also provides a testable framework to study the diversity relationships between predator and prey.