Large-scale green tides have broken out annually in the Yellow Sea since 2007, which, upon twinning with floating Sargassum horneri, became a new hazard and increased the difficulty of preventing and controlling the green tide in Shandong Peninsula. In this study, the similarity of ITS and coxI sequences were analyzed using S. horneri samples collected from ten free-floating populations and three benthic populations in 2016 and 2017 along the offshore of China. The results showed that the coxI sequences of 51 samples were consistent, while there were two variable nucleotide sites within the ITS sequence. Based on genotypic differences, S. horneri samples could be sorted into four categories, among which the genotype of free-floating samples from Dalian Longwangtang, Daqin Island, and Nanhuangcheng Island of Yantai were identical. Free-floating samples from the Golden Beach of Qingdao and benthic samples from Daqin Island of Yantai and Zhangzi Island of Dalian were identical; free-floating samples from Lidao of Weihai and Dongtou of Wenzhou were identical; and free-floating samples from the Sculpture Garden, Wanggezhuang, Dazhushan of Qingdao, Rushan of Weihai, and benthic samples from Gouqi Island were identical. However, there was no difference in genotype among individuals within the same population, even among those occurring in different years. A phylogenetic tree based on ITS sequences of S. horneri showed that samples from China were clustered together; however, there was some genetic distance from the Korean samples. It is possible that the genetic variation of ITS and coxI regions is low in different coastal strains of S. horneri, and that drifting population could be of different origins. These findings will provide a basis for further understanding of the molecular genetic background of S. horneri along the offshore of China.