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Green tides are a serious global ecological disaster; the largest occur in the Southern Yellow Sea (SYS). Early-stage green tides in the SYS are composed of four species (<i>Ulva prolifera</i>, <i>Ulva flexuosa</i>, <i>Ulva linza</i>, and <i>Ulva compressa</i>). We found that <i>U. aragoensis</i> is a constituent species of green tides in the SYS based on molecular data. Furthermore, this study re-evaluated the proportion of <i>U. aragoensis</i> in green tides and found that it was more prevalent in micro-propagules cultured from surface seawater during an early-stage green tide in 2021. The internal transcribed spacers, <i>tuf</i>A, 18S, <i>rbc</i>L, large subunit, <i>psb</i>A, and rps2-<i>trn</i>L gene sequences were compared; the <i>tuf</i>A and <i>rbc</i>L gene sequences were the most suitable DNA barcodes for distinguishing <i>U. aragoensis</i>. A haplotype analysis of the sequences of floating <i>U. aragoensis</i> and its micro-propagules was performed to study the correlation between green tide macroalgae and micro-propagules; close haplotype similarities occurred between them. This study further clarified the species composition of SYS green tides and provided a reference for assessing the relationship between micro-propagules and green tide macroalgae.