Shell small, profile moderately high, one-half apical whorl retained in teleoconch before expansion to limpet shell form. Apical whorl nearly smooth. Protoconch bulbous, retained in adult shell on right side of apical whorl. Protoconch microsculpture of deep, closely spaced pits, visible only under high magnification. Foramen subapical, outline of foramen broadly triangular; selenizone greatly reduced, septum straight, high. Mature sculpture finely clathrate, with low beads at intersections (in most species).
Epipodial tentacles reduced, consisting of one large posterior pair, one smaller lateral-posterior pair, and one smaller posterior pair. Gill bipectinate with free axis.
Rachidian tooth with long shaft and broader base; overhanging tip deeply serrate; shafts and cusps of lateral teeth similar to those of rachidian; cusps of fourth lateral reduced; pluricuspid large, with acutely tapered tip and inner and outer cusps near bend.

Profundisepta has characters of protoconch form, protoconch sculpture, and early whorl that differ from those of Manganesepta. The posterior pedal tentacle of Manganesepta is lacking. The pitted microsculpture of the protoconch is unique among the genera treated here. The bulbous form of the protoconch is shared with that of Fissurisepta, although the apex is unlike that of Fissurisepta, in which the apical whorl is lost in mature specimens. Shell sculpture differs among the species assigned to the genus.