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An outbreak of Ulva prolifera poses a massive threat to coastal ecology in the Southern Yellow Sea, China (SYS). It is a necessity to extract its area and monitor its development accurately. At present, Ulva prolifera monitoring by remote sensing imagery is mostly based on a fixed threshold or artificial visual interpretation for threshold selection, which has large errors. In this paper, an adaptive threshold model based on Google Earth Engine (GEE) is proposed and applied to extract U. prolifera in the SYS. The model first applies the Floating Algae Index (FAI) or Normalized Difference Vegetation Index (NDVI) algorithm on the preprocessed remote sensing images and then uses the Canny Edge Filter and Otsu threshold segmentation algorithm to extract the threshold automatically. The model is applied to Landsat8/OLI and Sentinel-2/MSI images, and the confusion matrix and cross-sensor comparison are used to evaluate the accuracy and applicability of the model. The verification results show that the model extraction of U. prolifera based on the FAI algorithm has higher accuracy (R2 = 0.99, RMSE = 5.64) and better robustness. However, when the average cloud cover is more than 70% in the image (based on the statistical results of multi-year cloud cover information), the model based on the NDVI algorithm has better applicability and can extract the algae distributed at the edge of the cloud. When the model uses the FAI algorithm, it is named FAI-COM (model based on FAI, the Canny Edge Filter, and Otsu thresholding). And when the model uses the NDVI algorithm, it is named NDVI-COM (model based on NDVI, the Canny Edge Filter, and Otsu thresholding). Therefore, the final extraction results are generated by supplementing NDVI-COM results on the basis of FAI-COM extraction results in this paper. The F1-score of U. prolifera extracted results is above 0.85. The spatiotemporal distribution of U. prolifera in the South Yellow Sea from 2016 to 2020 is obtained through the model calculation. Overall, the coverage area of U. prolifera shows a decreasing trend over the five years. It is found that the delay in recovery time of Porphyra yezoensis culture facilities in the Northern Jiangsu Shoal and the manual salvage and cleaning-up of U. prolifera in May are among the reasons for the smaller interannual scale of algae in 2017 and 2018. [ABSTRACT FROM AUTHOR]