- waageni, Squamularia
- Waagenoconcha, genus
- Waagenoperna hayamii
- Waagenophyllum, genus
- Waagenophyllum akasakensis
- Waagenophyllum indicum
- wadanum, Rhododendron
- wakasana, Spiriferina
- wakimizui, Naticopsis
- wakinoensis, Brotiopsis
- wakinoensis, Endophycus
- Wakinoichthys aokii
- Wakinoichthys robustus
- Wakinosaurus satoi
- wakitai, Jacus
- wakitai, Napora
- wakuyaensis, Nipponopecten
- wakuyaensis, Placopecten
- Walking dendro
- Wallucina lamyi
- Wallucina striata
- Walnut tree
- wardiana, Kennerlia
- wardiana, Pandora
- wardiana, Pandora (Kennerlia)
- wardiana, Pandorella
- Warnstorfia moss
- wasabidaniensis, Retiophyllia
- Washington clam
- Washitaster macroholcus
- watanabei, Anadara
- watanabei, Arca
- watanabei, Dentalium
- watasei, Eumetopias
- watasei, Oriensarctos
- watasei, Portlandia
- watasei, Portlandella
- Watermoss
- Water-shield