Since 2007, large-scale green tides dominated by Ulva prolifera consecutively bloomed in the Yellow Sea and caused great economic losses. The fouling U. prolifera on the Pyropia yezoensis aquaculture rafts in the Subei Shoal was regarded as the major source of the floating biomass. However, it was still unclear about the seed source of fouling green macroalgae attached on the rafts. In this study, the field surveys and the indoor experiments were conducted to reveal the source of propagules of the fouling green macroalgae on the rafts and to study the anti-fouling material for P. yezoensis aquaculture rafts which could possibly be a feasible strategy to control the green tides in the Yellow Sea. The results showed that (1) micro-propagules of several green macroalgal species, including U. prolifera, U. linza, U. compressa, U. flexuosa, and Blidingia sp. coexisted in the waters and sediments in the Subei Shoal and their proportion remarkably changed over time; (2) the bamboo poles with peeling treatment could significantly reduce the amount of U. prolifera micro-propagules attached. This study confirmed that the micro-propagules distributed in the Subei Shoal area were the precursors of the green tides, and provided a feasible method to control the Yellow Sea large-scale green tides at the beginning.