Lithogenes is the only genus within the subfamily Lithogeneinae. This genus and subfamily, the most basal group in Loricariidae, is the sister group to the rest of the family. Relative to an undescribed species of Lithogeneinae, L. valencia has sister group relationship to L. villosus.
The three recognized species in this genus are: 
- Lithogenes valencia Provenzano, Schaefer, Baskin & Royero-Leon, 2003
- Lithogenes villosus Eigenmann, 1909
- Lithogenes wahari Schaefer & Provenzano, 2008
Appearance and anatomy
As members of Loricariidae, Lithogenes species have a suckermouth. However, unlike most loricariids, Lithogenes possesses armor plating only on the latter half of the body. Their eyes are small and their bodies flattened.
Distribution and habitat
L. villosus originates from the Essequibo River drainage of the Guiana Shield. An undescribed species of Lithogenes is known from the Orinoco basin of the Guiana Shield. L. valencia has only been known from six specimens collected in the 1970s from tributaries of the Lake Valencia in northern Venezuela; however, this area has since been polluted and this species possibly is now extinct.
- Schaefer, Scott A. (2003). "Relationships of Lithogenes villosus Eigenmann, 1909 (Siluriformes, Loricariidae): Evidence from High-Resolution Computed Microtomography" (PDF). American Museum Novitates (American Museum of Natural History) 3401: 1–55. doi:10.1206/0003-0082(2003)401<0001:ROLVES>2.0.CO;2. ISSN 0003-0082.
- Provenzano R., Francisco; Schaefer, Scott A.; Baskin, Jonathan N.; Royero-Leon, Ramiro (2003). Buth, D. G., ed. "New, Possibly Extinct Lithogenine Loricariid (Siluriformes, Loricariidae) from Northern Venezuela" (PDF). Copeia (American Society of Ichthyologists and Herpetologists) 2003 (3): 562–575. doi:10.1643/CI-02-160R1.
- Froese, Rainer, and Daniel Pauly, eds. (2011). Species of Lithogenes in FishBase. December 2011 version.
- Froese, Rainer and Pauly, Daniel, eds. (2007). "Lithogenes villosus" in FishBase. May 2007 version.