• Caloneis P. Cleve, 1894
• Caloneis abnormis (Grunow) Cleve
• Caloneis absoluta Manguin
• Caloneis achnanthiformis Cleve-Euler
• Caloneis adenensis Cleve
• Caloneis advena Van Landingham
• Caloneis aemula
• Caloneis aequatorialis Hustedt
• Caloneis aerophila Bock, 1962
• Caloneis africana (M.H. Giffen) S.R. Stidolph
• Caloneis allorgei Manguin
• Caloneis alpestris (Grunow) Cleve, 1894
• Caloneis amica (Cleve & Grunow) Cleve
• Caloneis amphicephala Hustedt
• Caloneis amphigomphus Jurilj
• Caloneis amphisbaena (Bory de Saint Vincent) Cleve, 1894
• Caloneis andersonii (Cleve) Cleve
• Caloneis angustivalva J.B. Petersen, 1928
• Caloneis arctica (Krasske) H. Lange-Bertalot
• Caloneis austrogeorgica Carlson, 1913
• Caloneis bacillaris (W. Gregory) Cleve
• Caloneis bacillum (Grunow) Cleve, 1894
• Caloneis bacillum (Grunow) Mereschkowsky
• Caloneis backmanii A. Cleve in Backman & A Cleve, 1922
• Caloneis baikalensis Skvortzov & Meyer
• Caloneis baltica
• Caloneis balticum (Cleve-Euler) Schulz
• Caloneis bannajensis Petersen
• Caloneis barrowiana Patrick & Freese
• Caloneis beccariana (Grunow) Cleve
• Caloneis biclavata Cleve & Grove
• Caloneis biconfusa (Bourrelly & Manguin) Van Landingham
• Caloneis biconstricta (Grove & Sturt) Cleve
• Caloneis bicuneata (Grun.) Cleve, 1894
• Caloneis bicuneata (Grunow) Boyer, 1927
• Caloneis binotata Cleve-Euler
• Caloneis biseriata (Petit) Cleve
• Caloneis bivittata (Pantocsek) Cleve, 1894 accepted as Caloneis permagna (J.W. Bailey) Cleve, 1894
• Caloneis blanda (A. Schmidt) Cleve, 1894 accepted as Navicula ergadensis (Gregory) Ralfs, 1861
• Caloneis bleischiana (Janisch & Rabenhorst) Boyer
• Caloneis borealis J.R. Carter, 1971
• Caloneis bottnica Cleve
• Caloneis bourrellyi Fusey
• Caloneis branderii (Hustedt) Krammer, 1985
• Caloneis brasiliensis Heiden
• Caloneis brevis (Gregory) Cleve, 1894
• Caloneis bryophila Manguin ex Kociolek & Reviers
• Caloneis budensis (Grunow) Krammer, 1985
• Caloneis butantana Krasske
• Caloneis callosa Åke Berg
• Caloneis campbellii (Petit) Cleve, 1894
• Caloneis castracanei (Grunow) Cleve
• Caloneis chasei Cholnoky
• Caloneis clevei (N. Lagerstedt) Cleve
• Caloneis constans E. Reichardt
• Caloneis continua J.R. Carter, 1964
• Caloneis crassa (Gregory) R.R. Ross, 1986
• Caloneis delphineae Van de Vijver
• Caloneis densestriata (Pr.-Lavr.) Gusl.
• Caloneis desertorum Hustedt
• Caloneis digitus E.G. Jorgensen
• Caloneis dorogostaiskyi (Østrup) M.B. Edlund, N. Soninkhishig, R.M. Williams & E.F. Stoermer
• Caloneis dubia Krammer, 1987
• Caloneis dumbeana R. Maillard
• Caloneis egena (A. Schmidt) Cleve
• Caloneis elongata (Grunow) Boyer
• Caloneis excentrica (Grunow) C.S. Boyer, 1927
• Caloneis eximia Grunow accepted as Navicula eximia (Grunow) Grunow, 1897
• Caloneis falcifera H. Lange-Bertalot, Genlkal & Vekhov
• Caloneis fasciata (Lagerstedt) Cleve, 1894 accepted as Caloneis bacillum (Grunow) Cleve, 1894
• Caloneis fenzlii (Grunow) Patrick, 1966
• Caloneis fontinalis (Grunow) Cleve-Euler, 1932
• Caloneis fontinalis (Grunow) H. Lange-Bertalot & Reichardt, 1996
• Caloneis formosa (Gregory) Cleve, 1894 accepted as Caloneis westii (W. Smith) Hendey, 1964
• Caloneis fossilis Cleve-Euler
• Caloneis frasnensis Fusey
• Caloneis frigida Foged
• Caloneis furcata Cleve-Euler
• Caloneis fusioides (Grunow) Heiden & Kolbe, 1928
• Caloneis fusoides (Grunow) Heiden & Kolbe, 1928
• Caloneis gjeddeana Foged, 1976
• Caloneis glaberrima Østrup, 1910
• Caloneis gracilis H.P. Gandhi
• Caloneis guadalupensis Bourrelly & Manguin
• Caloneis hardmaniana Cleve, 1894
• Caloneis hebes (Ralfs) R.M. Patrick, 1966 accepted as Caloneis obtusa (W. Smith) Cleve, 1894
• Caloneis heimii Bourrelly & Manguin
• Caloneis hendeyi H. Lange-Bertalot
• Caloneis hexapla (Schmidt) F.W. Mills, 1933
• Caloneis hitoyosiensis H. Okuno
• Caloneis holstii (Cleve) Cleve
• Caloneis hustedtii Aleem, 1951
• Caloneis hyalina Hustedt, 1937
• Caloneis incognita Hustedt
• Caloneis inliberalis J.R. Carter & P. Denny
• Caloneis intermedia H.P. Gandhi
• Caloneis jonssoni Østrup
• Caloneis kateri Metzeltin, H. Lange-Bertalot & García-Rodríguez
• Caloneis kristinae Gerd Moser
• Caloneis kryophila Cleve