Background: The fishes of family Gobiidae are one of the least studied fishes, especially for otolith structure. The otoliths were possess species specific features. Hence, traits of sagittal otolith of gobid species studied. Methods: Five gobid species Odontamblyopus roseus (Valenciennes, 1837), Trypauchen vagina (Bloch and Schneider, 1801), Glossogobius giuris (Hamilton, 1822), Parachaeturichthys polynema (Bleeker, 1853) and Boleophthalmus dussumieri (Valenciennes, 1837) were investigated by three methods including morphological, shape indices and step wise discriminant function analysis (SDFA). Result: Interrelationship between shape indices investigated, at 95% level of confidence (P less than 0.05), revealed that perimeter of P. polynema and area of T. vagina have isometric growth with their length (b = 3.0071, 2.90, respectively) and otolith area of B. dussumieri have positive allometric growth (b = 4.23077). SDFA, based on otolith morphometry, discriminated species up with 97.18% accuracy. Hence, the results of present investigation can be used for discrimination of the species and as a tool in predicting fish size from the otoliths and in calculating the biomass of these less studied fish species.