The Emerald Goby can be distinguished from the Freshwater Goby, Frillfin Goby, Green Goby, Naked Goby, and Seaboard Goby by its notably elongated lanceolate caudal fin. The Emerald Goby's pattern consists of ringed small greenish spots, midline and dorsal blotches, and a dark shoulder marking above the base of the pectoral fin. The Violet Goby and Highfin Goby which share the Emerald Goby's lanceolate caudal fin shape can be discerned by differences in body patterning. The Violet Goby is marked by a repeating pattern of dark vertical chevron markings and the Highfin Goby possesses a large ocellated spot below its first dorsal fin and another pronounced dark spot at the base of its caudal fin.