From 2008 to 2016, massive floating green macroalgal blooms occurred annually during the summer months in the Yellow Sea. The original source of these blooms was traced based on the spatio-temporal distribution and species composition of Ulva microscopic propagules and settled Ulva vegetative thalli monthly from December 2012 to May 2013 in the Yellow Sea. High quantities of Ulva microscopic propagules in both the water column and sediments were found in the Pyropia aquaculture area along the Jiangsu coast before a green macroalgal bloom appeared in the Yellow Sea. The abundance of Ulva microscopic propagules was significantly lower in outer areas compared to in Pyropia aquaculture areas. A molecular phylogenetic analysis suggested that Ulva prolifera microscopic propagules were the dominant microscopic propagules present during the study period. The extremely low biomass of settled Ulva vegetative thalli along the coast indicated that somatic cells of settled Ulva vegetative thalli did not provide a propagule bank for the green macroalgal blooms in the Yellow Sea. The results of this study provide further supporting evidence that the floating green macroalgal blooms originate from green macroalgae attached to Pyropia aquaculture rafts along the Jiangsu coastline of the southern Yellow Sea.