We studied fossil diatom flora of sediments within the Gamo Formation of the Kobiwako Group, located in eastern Shiga, Central Japan. The sediments were determined to deposit Early Pleistocene, about 1.8–1.9 Ma. Diatoms collected from 11 horizons were taxonomically examined using light and scanning electron microscopies. We found 150 species belonging to 46 genera, but 33 species among them remained unidentified. Aulacoseira ambigua, Staurosira construens, and Staurosira venter var. binodis, were abundant in the samples. Among the species identified, Navicula hasta sensu stricto is probably extinct, but the others were all extant. Species belonging to Fragilaria sensu lato were intensively examined, and twenty-six species were identified, although six of them remained unidentified. Some of these unidentified species did not conform to similar extant ones in their dimensions, suggesting they include extinct species.

The marine diatom, Thalassiothrix antarctica, has a circum-Antarctic distribution in the modern ocean, whereas T. longissima prefers cold-water regions in the northern hemisphere. This different distribution has been thought to apply to their fossil record as well. An examination of upper Pliocene to lower Pleistocene sediments from the subpolar North Atlantic, however, has revealed abundant specimens of T. antarctica but none of T. longissima. These specimens of T. antarctica are characterized by morphological heteropolarity: a head-pole with two apical spines and a rimoportula at the end of an areolar area; a foot-pole with no spines and a rimoportula on a hyaline foot apex. Additionally, the specimens have a twisted, sigmoidally curved outline in the middle, a specific characteristic of T. antarctica. The late Pliocene to the early Pleistocene was a transitional period that led to the formation of continental ice sheets in northern high latitudes and onset of pronounced glacial-interglacial cycles. Concomitant oceanographic changes at that time may have resulted in the disappearance of T. antarctica in the northern hemisphere.

Larger marine diatom fossils were examined from 12 samples collected from Neogene marine sediments distributed in the northern and central areas of Honshu Island, Japan. The diatoms were separated into smaller and larger sizes through a sieve of 63 µm. Depositional ages were determined for the samples on the basis of the Neogene North Pacific diatom biochronology of smaller diatoms, ranging from the diatom zones NPD3A (uppermost, 16.6–16.7 Ma), NPD4A (15.8–15.9 Ma, 14.6–14.8 Ma), NPD5C (10.0–11.4 Ma) and NPD7Bb (3.5–5.5 Ma). Fifty-three larger diatom taxa in 23 genera were identified including 42 typical larger diatom taxa in 17 genera. Typical larger diatoms are: Triceratium (10 taxa), Aulacodiscus (6 taxa), Biddulphia (5 taxa), Actinocyclus (3 taxa), Coscinodiscus (3 taxa), Auliscus (2 taxa), Campylodiscus (2 taxa), Isthmia (2 taxa) and Arachnoidiscus, Cerataulus, Craspedodiscus, Endictya, Hyalodiscus, Leudugeria, Rutilaria, Sticutodiscus and Surirella (1 taxon each). Forty-eight larger diatoms are shown in plates with remarks on 17 taxa. This study has elucidated the general compositions of Neogene larger marine diatom assemblages in Japan, which are completely different from those of smaller diatom assemblage.

Two new Tertiarius taxa, proposed as T. kabutoiwaensis sp. nov. and T. minimus sp. nov., were described from a freshwater Pliocene crater lake deposit in the Kabutoiwa Formation, Gunma Prefecture, central Japan. The two new taxa have a single rimoportula associated with a mantle fultoportula-bearing costa, a charecteristics of the genus Tertiarius. In addition, T. kabutoiwaensis is characterized by radial areolae rows on valve face, one valve face fultoportula, mantle with a total of 5–15 costae each having a mantle fultoportula. T. minimus is characterized by its very small size, slightly elliptical openings of areolae on marginal valve face and mantle, one valve face fultoportula and a total of 3–6 costae, each with a mantle fultoportula. These two new species are compared to Tertiarius oitaensis from the Omoto Formation, Oita Prefecture and T. satsumaensis from the Koriyama Formation, Kagoshima Prefecture, southwestern Japan. All four Tertiarius taxa, as well as Cyclotella notata from the Omoto Formation are shown herein.

We investigated the benthic diatom flora of the intertidal shore in Tokyo Bay, Japan. Sediment samples were collected from 15 intertidal flats and beaches during several ebb tides in May 2010. The salinity ranged from 10.6 to 30.5. A total of 88 taxa occurred from the 15 sampling sites. For each site, the number of species identified ranged from 9 to 33, with the exception of one site that contained the coarse-grained sediment and at which diatoms were not observed. The dominant taxa (those with relative abundances of more than 10%) were mainly species of Navicula and Amphora. The species observed at the largest number of sites was Navicula gregaria; the second most widespread were Haslea feriarum and Fallacia cf. teneroides. Most of the species in Tokyo Bay are cosmopolitan, thus, benthic diatom flora in intertidal flat would be affected by specific environments of intertidal flats, such as drying and drastic changes of temperature and salinity by the tidal fluctuation.