Siphonogobius nue is a species of goby native to the coastal waters of Japan where it occurs on sandy substrates with rocks or artificial structures for concealment. A shallow water fish, it is found at depths of from 1 to 2 metres (3.3 to 6.6 ft). Males of this species grows to a length of 9.2 centimetres (3.6 in) SL while the females only reach 8.3 centimetres (3.3 in) SL. This species is the only known member of its genus.