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<i>Sargassum horneri</i> golden tides are increasingly becoming a marine ecological problem in the Yellow Sea (YS) and East China Sea. To understand the genetic relationship between the attached <i>S. horneri</i> along the China coast and the floating biomass in the YS, we used partial <i>rbcL</i>, <i>ITS2</i>, <i>cox1</i>, <i>cox3</i>, and <i>cob-cox2</i> to analyze the population genetic evolution of 165 <i>Sargassum</i> samples. The results showed that all samples were a single species of <i>S. horneri</i>. Partial sequences of each gene had major haplotypes, and other haplotypes evolved from the occurrence of base mutations. The <i>cob-cox2</i> gene haplotype research showed only the attached samples from ZJ, LN, and KR contained Hap3, and the distribution proportions of Hap2 and Hap4 in SS and the YS were closest to the distribution of the attached samples from SD. These novel findings provided information about the genetic evolutionary relationship between attached <i>S. horneri</i> along the coast of China and floating <i>S. horneri</i> in the YS, as well as new ideas for tracing the source of floating <i>S. horneri</i> in the YS from a molecular biological perspective.