• Protodrilus Czerniavsky, 1881 (uncertain > nomen dubium)
• Protodrilus Hatschek, 1881
• Protodrilus adhaerens Jägersten, 1952 accepted as Meiodrilus adhaerens (Jägersten, 1952)
• Protodrilus adhaerens f. gracilis Jouin, 1968 accepted as Protodrilus gracilis von Nordheim, 1989 accepted as Meiodrilus gracilis (von Nordheim, 1989)
• Protodrilus adhaerens f. major Jouin, 1970 accepted as Protodrilus adhaerens Jägersten, 1952 accepted as Meiodrilus adhaerens (Jägersten, 1952)
• Protodrilus affinis Jouin, 1968
• Protodrilus albicans Jouin, 1970
• Protodrilus bahuriensis [auct.] accepted as Protodrilus bahusiensis Jägersten, 1952 accepted as Protodrilus oculifer Pierantoni, 1908
• Protodrilus bahusiensis Jägersten, 1952 accepted as Protodrilus oculifer Pierantoni, 1908
• Protodrilus brevis Jouin, 1970
• Protodrilus chaetifer Remane, 1926 accepted as Protodriloides chaetifer (Remane, 1926)
• Protodrilus ciliatus Jägersten, 1952
• Protodrilus corderoi du Bois-Reymond Marcus, 1948 accepted as Claudrilus corderoi (du Bois-Reymond Marcus, 1948)
• Protodrilus draco Martínez, Di Domenico, Jörger, Norenburg & Worsaae, 2013 accepted as Claudrilus draco (Martínez, Di Domenico, Jörger, Norenburg & Worsaae, 2013)
• Protodrilus flabelliger Wieser, 1957 accepted as Claudrilus flabelliger (Wieser, 1957)
• Protodrilus flavocapitatus (Uljanin, 1877) accepted as Lindrilus flavocapitatus (Uljanina, 1877)
• Protodrilus gelderi Riser, 1997
• Protodrilus gracilis von Nordheim, 1989 accepted as Meiodrilus gracilis (von Nordheim, 1989)
• Protodrilus hatscheki Pierantoni, 1908
• Protodrilus haurakiensis von Nordheim, 1989 accepted as Lindrilus haurakiensis (Von Nordheim, 1989)
• Protodrilus helgolandicus von Nordheim, 1983 accepted as Claudrilus helgolandicus (von Nordheim, 1983)
• Protodrilus helgolendicus [auct.] accepted as Protodrilus helgolandicus von Nordheim, 1983 accepted as Claudrilus helgolandicus (von Nordheim, 1983)
• Protodrilus hochbergi Martínez, Di Domenico, Jörger, Norenburg & Worsaae, 2013
• Protodrilus huanghaiensis Wu, Sun & Chen, 1980
• Protodrilus hypoleucus Armenante, 1903 accepted as Claudrilus hypoleucus (Armenante, 1903)
• Protodrilus hypoleucus f. tenuis Jouin, 1968 (uncertain > nomen dubium)
• Protodrilus indicus Aiyar & Alikuhni, 1944 accepted as Meiodrilus indicus (Aiyar & Alikuhni, 1944)
• Protodrilus infundibuliformis Schmidt & Westheide, 1977
• Protodrilus jagersteni von Nordheim, 1989
• Protodrilus jägersteni [auct.] accepted as Protodrilus jagersteni von Nordheim, 1989
• Protodrilus jouinae von Nordheim, 1989 accepted as Meiodrilus jouinae (von Nordheim, 1989)
• Protodrilus leuckarti [auct.] accepted as Protodrilus leuckartii Hatschek, 1881
• Protodrilus leuckartii Hatschek, 1881
• Protodrilus litoralis von Nordheim, 1989
• Protodrilus minutus Kirsteuer, 1966 accepted as Claudrilus minutus (Kirsteuer, 1966)
• Protodrilus mirabilis Czerniavsky, 1881 (uncertain > nomen dubium)
• Protodrilus oculifer Pierantoni, 1908
• Protodrilus oculifer borealis Remane, 1932 accepted as Protodrilus oculifer Pierantoni, 1908
• Protodrilus ovarium Di Domenico, Martínez, Lana & Worsaae, 2013 accepted as Claudrilus ovarium (Di Domenico, Martínez, Lana & Worsaae, 2013)
• Protodrilus pardii Gerlach, 1953 accepted as Protodrilus adhaerens Jägersten, 1952 accepted as Meiodrilus adhaerens (Jägersten, 1952)
• Protodrilus pierantonii Aiyar & Alikuhni, 1944 accepted as Claudrilus pierantonii (Aiyar & Alikuhni, 1944)
• Protodrilus puniceus Sato-Okoshi, Okoshi & Fujiwara, 2015
• Protodrilus purpureus (Schneider, 1868) accepted as Megadrilus purpureus (Schneider, 1868)
• Protodrilus pythonius Di Domenico, Martínez, Lana & Worsaae, 2013
• Protodrilus robustus Jägersten, 1952
• Protodrilus rubropharyngeus Jägersten, 1940 accepted as Lindrilus rubropharyngeus (Jägersten, 1940)
• Protodrilus schneideri (Langerhans, 1880) accepted as Megadrilus schneideri (Langerhans, 1880)
• Protodrilus similis Jouin, 1970 accepted as Claudrilus similis (Jouin, 1970)
• Protodrilus smithsoni Martínez, Di Domenico, Jörger, Norenburg & Worsaae, 2013
• Protodrilus sphaerulatus Pierantoni, 1908 accepted as Claudrilus hypoleucus (Armenante, 1903)
• Protodrilus spongioides Pierantoni, 1903
• Protodrilus submersus von Nordheim, 1989
• Protodrilus symbioticus Giard, 1904 accepted as Protodriloides symbioticus (Giard, 1904)
• Protodrilus ypoleucus [printer's error] accepted as Claudrilus hypoleucus (Armenante, 1903)