Anatoma japonica is a species of small sea snail, a marine gastropod mollusk or micromollusk in the family Anatomidae.
The length of the shell varies between 1 mm and 2.5 mm. It has a trochiform shell. The spire contains 3ý rather convex whorls. They are finely decussated by elevated longitudinal striae and close striae. The longitudinal striae are flexuous at the base. The aperture is subcircular. The outer lip is dilated and reflexed in the middle.
This marine species occurs in deep water off the Philippines, Japan, and Southeast Africa.