Names where authority is Werner
- Class: Amphibia
- Order: Anura
- Family: Alsodidae
- Family: Aromobatidae
- Family: Arthroleptidae
- Family: Batrachylidae
- Genus: Batrachyla
- Species: Batrachyla taeniata (Girard, 1855)
- Synonym: Borborocoetes taeniatus var. albovittata Werner, 1896
- Synonym: Borborocoetes taeniatus var. bilineata Werner, 1896
- Synonym: Borborocoetes taeniatus var. intermedia Werner, 1896
- Synonym: Borborocoetes taeniatus var. modesta Werner, 1896
- Synonym: Borborocoetes taeniatus var. ornata Werner, 1896
- Synonym: Borborocoetes taeniatus var. rufodorsata Werner, 1896
- Family: Brevicipitidae
- Family: Bufonidae
- Genus: Amietophrynus
- Genus: Atelopus
- Genus: Duttaphrynus
- Genus: Incilius
- Genus: Leptophryne
- Genus: Pseudobufo
- Genus: Rhaebo
- Genus: Rhinella
- Species: Rhinella limensis (Werner, 1901)
- Synonym: Bufo limensis Werner, 1901
- Species: Rhinella marina (Linnaeus, 1758)
- Synonym: Bufo pithecodactylus Werner, 1899
- Species: Rhinella rubropunctata (Guichenot, 1848)
- Synonym: Bufo spinulosus var. surda Werner, 1898
- Species: Rhinella schneideri (Werner, 1894)
- Synonym: Bufo schneideri Werner, 1894
- Species: Rhinella spinulosa (Wiegmann, 1834)
- Synonym: Bufo spinulosus var. aspera Werner, 1898
- Synonym: Bufo spinulosus var. ornata Werner, 1898
- Genus: Werneria
- Genus: Wolterstorffina
- Species: "Bufo" arabicus (Heyden, 1827)
- Synonym: Bufo viridis var. orientalis Werner, 1896
- Family: Craugastoridae
- Genus: Niceforonia
- Subfamily: Craugastorinae
- Subfamily: Pristimantinae
- Genus: Pristimantis
- Species: Pristimantis affinis (Werner, 1899)
- Synonym: Hylodes affinis Werner, 1899
- Species: Pristimantis appendiculatus (Werner, 1894)
- Synonym: Hylodes appendiculatus Werner, 1894
- Species: Pristimantis bogotensis (Peters, 1863)
- Synonym: Hylodes fasslianus Werner, 1916
- Species: Pristimantis frater (Werner, 1899)
- Synonym: Hylodes frater Werner, 1899
- Species: Pristimantis w-nigrum (Boettger, 1892)
- Synonym: Hylodes buergeri Werner, 1899
- Subfamily: Strabomantinae
- Family: Cycloramphidae
- Family: Dendrobatidae
- Family: Dicroglossidae
- Family: Hemiphractidae
- Family: Hylidae
- Subfamily: Hylinae
- Subfamily: Pelodryadinae
- Genus: Litoria Tschudi, 1838
- Synonym: Fanchonia Werner, 1893
- Species: Litoria amboinensis (Horst, 1883)
- Synonym: Hyla papuensis Werner, 1901
- Species: Litoria aurea (Lesson, 1826)
- Synonym: Fanchonia elegans Werner, 1893
- Synonym: Hyla aurea — Werner, 1897
- Species: Litoria infrafrenata (Günther, 1867)
- Synonym: Hyla dolichopsis var. pollicaris Werner, 1898
- Species: Litoria jeudii (Werner, 1901)
- Synonym: Hyla jeudii Werner, 1901
- Family: Hyperoliidae
- Family: Leptodactylidae Werner, 1896
- Family: Limnodynastidae
- Family: Mantellidae
- Family: Microhylidae
- Family: Myobatrachidae
- Family: Petropedetidae
- Family: Phrynobatrachidae
- Family: Ptychadenidae
- Genus: Ptychadena
- Species: Ptychadena aequiplicata (Werner, 1898)
- Synonym: Rana mascareniensis var. aequiplicata Werner, 1898
- Species: Ptychadena anchietae (Bocage, 1868)
- Synonym: Rana gondokorensis Werner, 1908
- Species: Ptychadena mascareniensis (Duméril and Bibron, 1841)
- Synonym: Rana venusta Werner, 1908
- Species: Ptychadena oxyrhynchus (Smith, 1849)
- Synonym: Ixalus bistrigatus Werner, 1894
- Species: Ptychadena schillukorum (Werner, 1908)
- Synonym: Rana schillukorum Werner, 1908
- Family: Pyxicephalidae
- Family: Ranidae
- Incertae Sedis: Rana temporaria var. nigromaculata Werner, 1897
- Genus: Hylarana
- Genus: Lithobates Fitzinger, 1843
- Genus: Odorrana
- Genus: Rana
- Species: Rana graeca Boulenger, 1891
- Synonym: Rana temporaria var. bosniensis Werner, 1897
- Species: Rana macrocnemis Boulenger, 1885
- Synonym: Rana Holtzi Werner, 1898
- Species: Rana ornativentris Werner, 1903
- Synonym: Rana japonica var. ornativentris Werner, 1903
- Species: Rana temporaria Linnaeus, 1758
- Synonym: Rana temporaria var. entzi Werner, 1897
- Synonym: Rana temporaria var. marmorata Werner, 1897
- Synonym: Rana temporaria var. nigromaculata Werner, 1897
- Family: Rhacophoridae
- Family: Rhinodermatidae
- Genus: Rhinoderma
- Species: Rhinoderma darwinii Duméril and Bibron, 1841
- Synonym: Rhinoderma darwinii var. angulata Werner, 1898
- Synonym: Rhinoderma darwinii var. lateralis Werner, 1898
- Synonym: Rhinoderma darwinii var. picta Werner, 1898
- Synonym: Rhinoderma darwinii var. unicolor Werner, 1898
- Family: Telmatobiidae
- Order: Caudata
- Order: Gymnophiona