| Caloneis latiuscula (Kütz.) Cleve, 1894 |
| Caloneis lauta Carter & Bailey-Watts, 1981 |
| Caloneis leptosoma (Grunow) Krammer, 1985 |
| Caloneis lewisii Patrick, 1945 |
| Caloneis lewisii var. inflata (Schultze) Patrick, 1966 |
| Caloneis liber (W. Sm.) Cleve, 1894 |
| Caloneis limosa (Kütz.) R.M. Patrick, 1966 |
| Caloneis linearis (Grunow) Boyer, 1927 |
| Caloneis mexicana Heiden, 1906 |
| Caloneis minuta (Grunow) T.Ohtsuja & Y.Fujita, 2001 |
| Caloneis molaris (Grunow) Krammer, 1985 |
| Caloneis oregonica (Ehrenb.) R.M. Patrick, 1966 |
| Caloneis patagonica (Cleve) Cleve, 1894 |
| Caloneis permagna (Bailey) Cleve, 1894 |
| Caloneis powelli (Lewis) Cleve, 1894 |
| Caloneis probabilis (A. Schmidt) Cleve, 1894 |
| Caloneis sabanicola E. Novelo, R. Tavera & C. Ibarra, 2007 |
| Caloneis schumanniana (Grunow) Cleve, 1894 |
| Caloneis silicula (Ehrenb.) Cleve, 1894 |
| Caloneis silicula var. elliptica Mayer, 1913 |