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.