Understanding prey-predator biodiversity relationship has been an important issue for ecology. Here, for the first time, we examined the biodiversity relationship between bacteria (prey) and nanoflagellates (predators) in the southern East China Sea. We obtained the bacterial and nanoflagellates biodiversity data through the sequences of 16S and 18S rRNA respectively with illumina Miseq, and abundance data by using flow cytometry and epiflouresnece microscopic counting, respectively. Our results indicate that bacteria and nanoflagellate biodiversities exhibit a positive relationship when all samples were included. However, when clustering samples based on nutrient conditions, the bacteria-nanoflagellates biodiversity relationship varies among different clustering groups. Also, the abundance of bacteria increased with increasing bacteria-nanoflagellates biodiversity ratio, suggesting that high diversity of prey hinders the grazing control of predators.