Yap diatoms—from freshwater streams through estuaries and mangroves to the marine coral reefs—had been sampled in 1988 and 2014 and a few species from the 1988 collections described in a 2009 report. The present paper documents 168 new records, including seven new species, mostly from coral reef habitats, but including some interesting new species from mangroves, and incorporates records published in taxonomic papers. In addition, 44 Mastogloia records were published separately, bringing the taxon total to 245. In the present paper, 32 records are new for Micronesia, while many others are species described from neighboring Guam in the past 15 years. The total represents probably less than one-quarter of the species present on the reef because many specimens of Navicula, Nitzschia, Amphora, etc., have so far been identified only to genus. Floristic studies of benthic diatoms are limited partly by the shortage of taxonomic studies, and we present the taxa for which we can make reasonable arguments for identification, supporting light microscopy with scanning electron micrographs whenever possible. New taxa include Ehrenbergiopsis gen. nov. for Ehrenbergiulva hauckii; Biddulphiella cuniculopsis sp. nov.; Campylodiscus tatreauae sp. nov.; Cymatoneis belauensis from Palau and Cymatoneis yapensis from Yap; Diploneis denticulata sp. nov.; Entomoneis yudinii sp. nov.; and Nitzschia pseudohybridopsis sp. nov. Interesting new records include: Achnanthes cf. brevipes; Actinocyclus decussatus; Caloneis ophiocephala; Licmophora cf. hastata; Lyrella cf. rudiformis; and an unidentified cymatosiroid. One sediment sample included the remains of a planktonic community with Chaetoceros peruvianus, Skeletonema grevillei, Thalassiothrix gibberula and two species of Lioloma, rarely seen in the oligotrophic waters of Micronesia.