A new mite species of the stigmaeid genus Eustigmaeus Berlese, 1910, E. asper sp. nov., is described from Honshu, Japan. Additionally, E. rhodomelus (Koch, 1841), which is broadly distributed in the Holarctic region, and E. pseudolacunus Khaustov, 2023, which was originally described from Russia, are recorded from Japan for the first time.