Aduncisulcus paluster is a free-living, unicellular flagellate belonging to the eukaryotic lineage Fornicata, which includes free-living and commensal/parasitic organisms. Here, we report the draft genome sequence of A. paluster, which provides clues for elucidating the adaptation to microaerophilic/anaerobic environments and the transition between free-living and commensal/parasitic lifestyles in Fornicata.