The present study enhances knowledge of the biodiversity of diatoms in Chuuk, Micronesia following our 2018 study on the seaweed-associated diatoms. We collected planktonic samples of diatoms from five sites of reef flats using a 20 μm mesh net, and two samples of seaweeds with epiphytes by hand from an islet on the barrier reef. In addition, the seaweed-associated diatoms from our 2018 study were analysed using scanning electron microscopy. A total of 109 diatom taxa are documented in the present study. Of these, 70 species were from net samples, and 39 species from the seaweed-associated diatoms. Thirty-one species are newly recorded from Micronesian waters. Most taxa are benthic or tychoplanktonic; euplanktonic diatoms were rare. The occurrence of benthic diatoms from the water column might be related to the Chuuk environmental conditions which include shallow water, strong light intensity and high grazing pressure, to which benthic diatoms seem to be able to better adapt than planktonic diatoms.