From 2007 to 2017, large-scale green tides occurred every year in the Yellow Sea of China, and Ulva prolifera was the main species leading to the green tide. In this study, we used the Polymerase chain reaction and 3’ Rapid-amplification of cDNA ends technique to amplify the nrDNA-LSU and IGS sequences in U. prolifera and one species of Blidingia. These techniques showed 3259 bp of nrDNA-LSU and 3388 bp of IGS in U. prolifera and 3282 bp nrDNA-LSU and 3059 bp IGS in Blidingia sp. At the same time, tandem repeats, short dyads, palindromic and multiple simple repeat sequences in the IGS sequence were found by analyzing the structure of the IGS sequence in U. prolifera and Blidingia sp. G + C contents of the IGS sequence in U. prolifera and Blidingia sp. were 52.42% and 53.09%, respectively. We divided the U. prolifera into two types according to the morphological characteristics. Although the specimens of U. prolifera from the Qingdao coastal area, Jiangsu coastal area and the Yellow Sea have different morphologies, their ITS and IGS sequences are almost identical. Therefore, the main species of the green tides in the Qingdao coastal area, Jiangsu coastal area and the Yellow Sea are the same and have the same origin.