Yongle Blue Hole located in Xisha Islands, South China Sea, is the deepest blue hole among all known ones in the world. Its special hydrological, geological and chemical characteristics, particularly the existence of anoxic and aphotic layer shaped the ecosystem. As the first attempt, an integrated survey of Yongle Blue Hole and its adjacent waters including lagoon and outer reef slope was conducted in March, 2017, in which diel vertical distribution of both zooplankton and phytoplankton was examined. The deep chlorophyll maxima shifted from 40m at daytime to 20m at night, and Chl-a was undetectable under 90m. For microphytoplankton, 55 taxa from 5 phyla were identified, among which Bacillariophyta had the highest species richness (34 taxa) while Dinophyta was the most abundant (~54.9%). For picophytplankton, Synechococcus appeared mostly above 20m, Prochlorococcus was dominant beneath 40m (81.5-87.2%). The vertical distribution and diurnal pattern of phytoplankton was in concert with that of Chl-a. For zooplankton, a total of 42 taxa and 14 planktonic larvae types were identified in Yongle Blue Hole, which shared 16 common taxa with the lagoon with higher biodiversity in terms of both evenness and richness, while species composition of the outer reef slope differed significantly from that of the other two locations, thus was considered a different community. Cyclopoid copepod Oithona attenuate was the dominant species at both daytime (43.4%) and nighttime (71.0%) in Yongle blue hole, followed with O. rigida (21.4%, daytime) and Scolecithricella longispinosa (12.0%, nighttime). The maximum abundance of zooplankton was observed at the depth of 60-90m in daytime, while at 20-40m in nighttime. The community at the depth of 0-20m in nighttime shared 60% similarity with that of 20-40m in daytime, which was also found between 20-60m in nighttime and 40-90m in daytime (68% similarity). The vertical distribution indicated the diel vertical migration of zooplankton, particularly copepods above the oxycline at 80-90m. However, the relatively high abundance of S. longispinosa (38.3 inds/m3) and O. attenuata (51.0 inds/m3) was also detected at the depth of 90-150m. How the plankton adapted to the special and isolated environment in the Yongle Blue Hole, particularly in the anoxic and aphotic zone needs further study by interdisciplinary approaches.