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This study compares five primary productivity algorithms for Korean waters. Five algorithms are in the form of vertical generalized production models: One algorithm is for gross primary production and four are for net primary production. The five algorithms were evaluated using 117 in situ primary production datasets observed by 20 cruises from 1994 to 2011 in Korean waters (East Sea, Yellow Sea, East China Sea, and Yeosu Bay). The results show that the regionally-tuned variants give better results than the original formulation. We recommend, among the tested algorithms, YSVGPM (Yellow Sea Vertically Generalized Productivity Model) for gross primary productivity algorithm and Kameda-Ishizaka algorithm for net primary productivity algorithm for estimating primary production in Korean waters.