A novel facultative anaerobic bacterivorous nanoflagellate was isolated from the water just below the permanent oxic-anoxic interface of the meromictic Lake Suigetsu, Japan. We characterized the isolate using light and transmission electron microscopy and molecular phylogenetic analyses inferred from 18S rDNA sequences. The phylogenetic analyses showed that the isolate belonged to class Placididea (stramenopiles). The isolate showed key ultrastructural features of the Placididea, such as flagellar hairs with two unequal terminal filaments, microtubular root 2 changing in shape from an arced to an acute-angled shape, and a lack of an x-fiber in root 2. However, the isolate had a single helix in the flagellar transition region, which is a double helix in the two known placidid nanoflagellates Placidia cafeteriopsis and Wobblia lunata. Moreover, the isolate had different intracellular features compared with these two genera, such as the arrangement of basal bodies, the components of the flagellar apparatus, the number of mitochondria, and the absence (or presence) of paranuclear bodies. The 18S rDNA sequence was also phylogenetically distant from the clades of the known Placididae W. lunata and P. cafeteriopsis. Consequently, the newly isolated nanoflagellate was described as Suigetsumonas clinomigrationis gen. et sp. nov.