The Ulva blooms have been observed at the coast of Gouqi Island, East China Sea recently, which was never reported before 2011. This study was designed to identify the species composition, phylogenetic correlation and geographical exchange of the two free-floating Ulva populations in the Yellow Sea and East China Sea. The results showed that the two populations were all consisted of Ulva prolifera (type 5S-A) and U. prolifera (type 5S-B) using ITS and 5S rDNA spacer region sequences. Based on the further sequence analysis, the samples in the East China Sea were genetically same with the green tide samples in the Yellow Sea, revealing that the two populations originated from one source. Besides, a numerical circulation modeling experiment confirmed that the Ulva blooms in the East China Sea had drifted from the Southern Yellow Sea. This study increases our understanding of the importance of controlling the spread of Ulva macroalgae blooms and their impacts.