Abstract This research investigated the distribution of Trichodesmium in the South China Sea and the ecological factors that affect it. The survey periods were from August 1999 to October 2000. A total of 5 cruises were conducted, mostly in summer and autumn, including cruise 559 (August 18~25, 1999), cruise 629 (May 22~27, 2000), cruise 588 (July 3~14, 2000), cruise 597 (October 4-13, 2000), and cruise 657 (October 16-21, 2000). The sampling stations were located on the continental shelves, the slope zones, and the basin in the South China Sea between 13~22∘N and 114~120∘E. The density of Trichodesmium in the South China Sea varied greatly among the continental shelves, the slope zones, and the basin zones. Trichodesmium density in the continental shelf and the slope was high, with an average density of 150¡Ó297¡Ñ103 trichomes/m3 (4~1008¡Ñ103 trichomes/m3) in the surface water and 151¡Ó322¡Ñ103 trichomes/m3 (13~1114¡Ñ103 trichomes/m3) in 2-60m water depth. This could be caused by the influence of the mixing of the Kuroshio water and the substances of terrestrial origin. In the basin, Trichodesmium density was low, with an average density of 5¡Ó7¡Ñ103 trichomes/m3 (0~22¡Ñ103 trichomes/m3) in the surface water and an average density of 6¡Ó7¡Ñ103 trichomes/m3(0~22¡Ñ103 trichomes/m3) in 2~60m water depth. The Trichodesmium communities are mainly composed of T. thiebautii and T. erythraeum, with T. thiebautii being more abundant than T. erythraeum. Their relative importance at the continental shelf and the slope zones was 58% and 36% respectively, and 64% and 31% in the basin respectively. Trichodesmium appeared commonly as a single trichome, rarely in colony. The vertical distribution of Trichodesmium concentrated at 0-100m. The highest density was near the surface, varying between 4~1008¡Ñ103 trichomes/m3. In summer, the Trichodesmium in the continental shelf and the slope zone of the South China Sea was slightly higher than that in the East China Sea. The influences of temperature, nutrient abundance and wind speed on the distribution of Trichodesmium are not obvious. Trichodesmium in shallow water became abundant after the passage of a typhoon. The maximum density of Trichodesmium was observed in shallow water and average number of trichome per colony decreased. The influences of the typhoon on Trichodesmium species composition and colony density were not obvious. High density of Trichodesmium occurred at shallow waters and the water column with low stratification index (SI) which repressed the properties of waters in the continental shelf and the slope zones. The regions in which high-density Trichodesmium appeared, were the continental shelves and slope which showed water properties similar to those of the Kuroshio water, indicating possible intrusion of the Kuroshio water in summer into the continental shelves and slope of the northern South China Sea.