The distribution features of Ulva microscopic propagules in Jiangsu Porphya aquaculture regions from Dec. 2012 to Apr. 2013 were investigated. The result showed that in each month the high density zone of the Ulva microscopic propagules in investigated areas were widely distributed in Rudong inshore Porphyra acquaculture regions. In the investigated areas, the temporal distribution features of the number of Ulva microscopic propagules presented the trend of rising gradually. From Dec.2012 to Apr.2013 the average number of Ulva propagules in investigated areas was 56,71,471,550 and 1 049 ind/L. By using ITS sequence and 5S rDNA intervening sequence analysis and construction of phylogenetic tree, the molecular results showed that compositions of microscopic propagules were Ulva prolifera and Ulva flexuosa. By analyzing the species composition of Ulva microscopic propagules, we found that 2-4 months before the breakout of green tide Ulva microscopic propagules of the dominant species in the Yellow Sea green tide became the dominant species in Jiangsu Porphyra aquaculture regions. A large number of Ulva microscopic propagules could germinate rapidly with the rising of temperature at the late spring. Therefore we speculated that a large number of Ulva microscopic propagules that existed in Porphyra aquaculture regions in Jiangsu would provide seed bank for Yellow Sea green tides.