Sanya Bay is located in the southernmost of Hainan Island, located 109 ° 20′-109 ° 30′E, 18°11′-18°18′N, with sea area of about 120 km2, and water depth from 5 to 20m, it is an open tropical bay, and also an important part of national coral reef reserve. Ciliates and environmental factors in coral reef waters in Sanya Bay were sampled and analyzed during August 22 to 26, 2004. Fifty-eight species of ciliates representing 33 genera, 14 orders and 6 classes (41,6,5,4,1and 1 one species, respectively from Spirotrichea, Phyllopharyngea, Litostomatea，Oligohymenophorea，Pseudociliatea and Prostomatea) were recorded., Tintinnids predominated in terms of species richness and numerical abundance, with 31 species Tintinnopsis minuta, T. bütschlii, T. tubolosa and T. tocantinencis were dominant followed by Strombidium tintinnodes, S. sulcatum and Laboea strobila. Generally, ciliates were more abundant and diverse in the bottom waters of Sanya Bay relative to surface waters, with average abundances of 375 cell/L and species 38 ciliates, 346 cell/L and 39 species in the bottom water and surface water, respectively. Surface waters were dominated by planktonic ciliates, primarily Tintinnina and Stombidiida. In contrast, ciliate species belonging to the orders Suctorida (such as Acineta sp.) and Peritrichida predominated in bottom waters, this is because the study area are shallow coral reef waters, coral substrate by the impact of accounting for a certain number of attached ciliates. The distribution of ciliate abundance at surface and bottom water show a similar trend, there are two orders of high-value areas, a high value area appears in the northwest central part between the Dongmao Island and the Ximao Island, another high value area appears in the Sanya River mouth. While the spatial distribution of chlorophyll a content had the similar trend of ciliate abundance. DOC concentrations in study waters are in high level, and accounting for 90% of TOC. Our results show that at stations with higher live coral cover, such as station S9, S4, and S7, the abundance of ciliates was significantly lower than other stations with little or low coral coverage. Suggesting the role of coral feeding on the ciliates are. There was a significant positive correlation between concentration of chlorophyll a (Chl a) and ciliate abundance. Our canonical correspondence analysis study also showed that there was a positive correlation between ciliates abundance and the DOC concentration. The DOC concentration was also correlated with bacterial biomass. Ciliates such as Eutintinnus fraknoii and Mesodinium pulex like to live in more suspended particles waters, while many species prefer to live in low suspended particles and the clear waters, as seen in Amphorellopsis acuta, Codonellopsis ostenfeldi and Helicostomella subulta etc. The Tontonia gracillima and Dadayiella acutiformis live environment with high PO4-P, while S. acutum and T. bütschlii like high chla water. Most of the other species live in low chlorophyll a waters, and with lower abundance, but also it can be seen, these ciliates are planktonic oceanic species. We conclude that Chl a, suspended solids, phosphate, and dissolved organic carbon are the main factors affecting the distribution of ciliates in the waters over the coral reef in Sanya Bay.