Abstract: In June and July, 2008, a large number of free-floating Enteromorpha were found in Qingdao coast, and it also happened in Lianyungang coast and Rudong coast, Jiangsu Province. The Enteromorpha samples were collected from Qingdao, Lianyungang and Rudong coasts, and their ITS and 18S rDNA genes were cloned and sequenced. Based on the sequence data of ITS and 18S rDNA, the molecular phylogenetic analysis was carried out. The result of the ITS sequence analysis showed that the similarity of ITS sequence between 5 samples (QD-01，QD-02，QD-03，LY-01，RD-02) was 100%. It indicated that main free-floating Enteromorpha species from Qingdao coast, Lianyungang coast and Rudong coast were the same species. The result was also supported by 18S rDNA sequence analysis. According to sequence similarity and BLAST analysis, there were another 2 species in free-floating Enteromorpha in Rudong. RD-01 belonged to Enteromorpha. The results of pairwise sequence divergency analysis showed that there was no difference between the main free-floating species from Qingdao, Lianyungang and Rudong coasts, and the values were very low (0.3%) between the free-floating Enteromorpha species and attached Enteromorpha species from Qingdao, Lianyungang and Rudong coasts.