In the Yellow Sea, large-scale green tides have broken out consecutively for eight years from 2007 to 2014. However, a small scale of floating brown algae appeared at the same time in coastal area of Shandong Peninsula, which gave more pressures including environmental impacts and economic losses. The 5.8S rDNA-ITS spacer regions of samples collected during the green tide were sequenced and analyzed. Multiple sequence alignment and phylogenetic analysis were performed to reveal the affinitybetween a Qingdao sample and four reported Sargassum samples. Our results indicated that the genetic identity of the algae from the green tide was of 99% similarity with Sargassum horneri from the coastal area of Zhejiang province and Jiangling, Korea. Phylogenetic analysis revealed that the floating sample clustered with Sargassum horneri closely, which proved the floating brown algae in Qingdao accompanied with green tides, was Sargassum horneri.