The species of the estuarine and freshwater gobiid fish genus Stigmatogobius are revised, and the genus defined. Stigmatogobius is a gobionelline characterised by a distinctive transverse pattern of infraorbital sensory papillae, a reduced headpore pattern which lacks an infraorbital pore and posterior oculoscapular canal, the first haemal spine curving around the second anal pterygiophore in several species, 17 segmented caudal rays and by having one more anal fin ray than in the second dorsal fin. Of the 18 nominal species in the genus, four are valid: S. borneensis, S. pleurostigma, S. sadanundio, and S. sella. Eleven species have been previously described as Stigmatogobius, with eight here assigned to Stigmatogobius, while the others are species of Redigobius, Mugilogobius, Eugnathogobuis or Pseudogobius. Two species, restricted to the Philippines and Borneo respectively, are described as new.