Acrocalanus pediger Cleve, 1901 accepted as Paracalanus clevei Carl, 1907 accepted as Paracalanus aculeatus Giesbrecht, 1888 represented as Paracalanus aculeatus aculeatus Giesbrecht, 1888 (original description)
Actinocyclus curvatulus (Grunow in A. Schmidt) Cleve, 1901 accepted as Coscinodiscus curvatulus var. curvatulus Grunow in Schmidt et al., 1878 (new combination reference)
Auricula punctata (Pantocsek) Cleve, 1901 accepted as Amphiprora punctata Pantocsek, 1892 (new combination reference)
Biddulphia pulchella var. grundleri (A. Schmidt) Cleve, 1901 accepted as Biddulphia gruendleri Schmidt in Schmidt et al., 1888 (new combination reference)
Calanopia aurivilli Cleve, 1901 (original description)
Calanopia aurivillii Cleve, 1901 accepted as Calanopia aurivilli Cleve, 1901 (original description)
Caloneis petitiana (Grunow) Cleve, 1901 accepted as Navicula petitiana Grunow in Cleve, 1881 (new combination reference)
Campylodiscus ecclesianus var. adriaticus (Grunow) Cleve, 1901 accepted as Campylodiscus adriaticus var. adriaticus Grunow, 1862 (new combination reference)
Campylodiscus ecclesianus var. debyi (Leuduger-Fortmorel) Cleve, 1901 accepted as Campylodiscus debyi Leuduger-Fortmorel, 1892 (new combination reference)
Campylodiscus ecclesianus var. pacifica (Grunow) Cleve, 1901 accepted as Campylodiscus pacificus Grunow in Schmidt et al., 1875 (new combination reference)
Campylodiscus normannicus var. wallichianus (Greville) Cleve, 1901 accepted as Campylodiscus wallichianus var. wallichianus Greville, 1863 (new combination reference)
Chaetoceros aequatorialis Cleve, 1873 (original description)
Chaetoceros aurivillii Cleve, 1901 (original description)
Chaetoceros calvus Cleve, 1901 (original description)
Endictya oceania var. minor (A. Schmidt) Cleve, 1901 accepted as Endictya minor Schmidt in Schmidt et al., 1881 (new combination reference)
Gyrosigma simile (Grunow) Cleve, 1901 accepted as Pleurosigma simile Grunow, 1880 (new combination reference)
Huttonia labuensis (Cleve) Cleve, 1901 accepted as Cerataulus labuensis var. labuensis Cleve, 1883 (new combination reference)
Lampriscus orbiculatus (Shadbolt) Cleve, 1901 accepted as Triceratium orbiculatum var. orbiculatum Shadbolt, 1854 (new combination reference)
Licmophora aurivillii Cleve, 1901 (original description)
Metacalanus Cleve, 1901 (original description)
Metacalanus aurivillii Cleve, 1901 (original description)
Navicula lyra f. robertsiana (Greville) Cleve, 1901 accepted as Navicula robertsiana f. robertsiana Greville, 1865 (new combination reference)
Navicula lyra f. signata (A. Schmidt in Schmidt et al.) Cleve, 1901 accepted as Navicula lyra var. signata Schmidt in Schmidt et al., 1874 (new combination reference)
Navicula lyra f. subcarinata (A. Schmidt in Schmidt et al.) Cleve, 1901 accepted as Navicula lyra f. subcarinata Grunow in Schmidt et al., 1874 (new combination reference)
Odontella affinis (Grunow) Cleve, 1901 accepted as Triceratium affine Grunow in Van Heurck, 1883 (new combination reference)
Odontella dubia (Brightwell) Cleve, 1901 accepted as Pseudictyota dubium (Brightwell) P.A. Sims & D. M. Williams in Sims et al., 2018 (new combination reference)
Odontella favus (Ehrenberg) Cleve, 1901 accepted as Triceratium favus f. favus Ehrenberg, 1840 (new combination reference)
Odontella spinulosa (Grunow) Cleve, 1901 accepted as Triceratium spinulosum Grunow in Schmidt et al., 1885 (new combination reference)
Pseudodiaptomus aurivillii Cleve, 1901 (original description)
Reticulina Cleve, 1901 accepted as Peltidium Philippi, 1839 (original description)
Reticulina aurivillii Cleve, 1901 accepted as Peltidium aurivillii (Cleve, 1901) (original description)
Rhizosolenia pellucida Cleve, 1901 (original description)
Rhizosolenia recta Cleve, 1901 (1902) (original description)
Sceptroneis aurivillii Cleve, 1901 (original description)
Streptotheca maxima Cleve, 1901 (original description)
Surirella fastuosa var. collare (A. Schmidt) Cleve, 1901 accepted as Surirella collare Schmidt in Schmidt et al., 1874 (new combination reference)
Surirella fastuosa var. exima (Greville) Cleve, 1901 accepted as Surirella eximia Greville, 1857 (new combination reference)
Surirella fastuosa var. fluminensis (Grunow) Cleve, 1901 accepted as Surirella fluminensis Grunow, 1862 (new combination reference)
Surirella fastuosa var. incurvata (A. Schmidt) Cleve, 1901 accepted as Surirella incurvata Schmidt in Schmidt et al., 1897 (new combination reference)
Surirella fastuosa var. kinkeri (A. Schmidt) Cleve, 1901 accepted as Surirella kinkeri Schmidt in Schmidt et al., 1897 (new combination reference)
Surirella fastuosa var. lorenziana (Grunow) Cleve, 1901 accepted as Surirella lorenziana f. lorenziana Grunow, 1862 (new combination reference)
Thalassiosira aurivillii Cleve, 1901 (original description)
Zygoceros chinensis (Greville) Cleve, 1901 accepted as Biddulphia chinensis Greville, 1866 (new combination reference)