Abstract: The Ulva prolifera green tide is one of the most severe ecological disasters in the southern Yellow Sea. The spatio-temporal distribution and population dynamics of U. prolifera micro-propagules are important parts of the regular monitoring of green tide in the Yellow Sea. However, the traditional culture method has long experimental period and low detection efficiency, which cannot satisfy the requirement of rapid monitoring and early warning. In this paper, a fluorescence quantitative PCR (qPCR) technique based on one 297 bp DNA fragment specific to the floating U. prolifera was developed to detect the U. prolifera micro-propagules. The artificially released U. prolifera gametes were used to study the copy number of the target gene fragment in U. prolifera cells (240 copies/cell). The water samples of Subei Shoal were collected in April 2023 and the abundances of U. prolifera micro-propagules were screened based on both qPCR and traditional culturing methods. The results showed that the average abundances of U. prolifera micro-propagules were 2.1×10⁷ copies/L (approximately 87 602 cells/L) and 6.5 inds/L by qPCR and traditional culturing method, respectively, and the abundances were higher in the near-shore water (around raft region) and lower in off-shore. The detection efficiency and the revealed distribution patterns of the U. prolifera micro-propagules were consistent through the two methods. This qPCR method is sensitive and efficient, and can be used for the regular monitoring on U. prolifera green tide in the Yellow Sea.