Abstract: In the present study, ciliate samples were collected from 10 sites in the estuary zones and 14 sites in the pe-lagic zones in the northern area of Lake Taihu in July 2009. The ciliate species and their horizontal distribution were analyzed with quantitative protargol stain (QPS) method. We also explored the relationship between the ciliate commu-nity compositions and the environmental variables. We observed 105 species that represented 60 genera, 15 orders and 3 classes. The numbers of the species in different order were counted and compared. Orders Haptorida (21 species) and Oligotrichida (20 species) ranked the first and second, followed by orders Prostomatida (12 species), Peritrichida (11 species), and Hypotrichida (11 species). These five orders were predominant in the samples, while less species belonged to the other ten orders Karyorelictida, Pleurostomatida, Colpodida, Nassulida, Cyrophorida, Suctoria, Hymenos-tomatida, Synhymeniida, Scuticociliatida, and Heterotrichida. Halteria bifurcate Tamar, H. grandinella Dujardin, Rimostrombidium brachykinetum Krainer, Tintinnopsis cylindrata Kofoid Campbell and Cyclidium glaucoma Mller were the dominant species in both estuary (3.1%-12.3% in abundance) and pelagic (4.5%-18.1%) zones, followed by Urotricha farcta Claparde Lachmann, Codonella cratera Leidy, R. humile Penard, Strombidium mirabile Penard, Tintinnidium pusillum Entz, Vorticella aquadulcis complex and V. campanula Ehrenberg. The abundance of ciliate was higher in the estuary zones than that in the pelagic zones, which fell in the range of 1600 to 80900 cells/L (average 31407 cells/L) and 1225 cells/L to 36000 cells/L (average 18618 cells/L), respectively. The biomass of ciliate showed the same pattern which was 1322.6 g/L and 543.6 g/L on average in the estuary and pelagic zones, respectively. Nei-ther the abundance nor the biomass of ciliates showed significant differences (P0.05). Among the functional feeding groups, bactivorous and algivorous ones were the most abundant in all the sites. With respect to the ciliate horizontal distribution pattern, both zones had similar dominant groups while ciliates in the estuary zones showed significantly higher biodiversity in Simpson's index, Margalef's index, Shannon's index and species richness (P0.05). Our results showed that the algivorous group was barely affected by the accumulated algae, but bacterivorous assemblage was positively correlated with chlorophyll a content (P0.001). These results implied that potentially there was a close relationship between the horizontal heterogeneity of ciliate community structures and the extent of cyanobacterial blooms.