This dataset recorded benthic diatoms attached to the diatom boards installed on the artificial floating islands (AFIs) in the seawater in Anping Historical Waterview Park, Tainan, Taiwan. Diatoms were cultured using diatom boards and sampled four times from October to December, 2017. A total of 45 diatom species belonging to 22 genera were identified. Among them, the Navicula genus was the highest in richness, and Achnanthes subsessilis and Nitzschia longissima dominated in number.