The scale morphology of a native goby, Awaous jayakari (Gobiidae) was studied using scanning electron microscopy and light microscopy. The morphological descriptions were based on the scale's type, shape, and features of the anterior, posterior, and lateral fields. Further characteristics of the focus, circuli, radii, lepidonts, and cteni, were investigated. Morphometric indices were calculated for some scales. Shape variability of scales was high in different regions. However, the majority of scales displayed a polygonal shape (hexagonal and pentagonal). Both ctenoid and cycloid scales were observed in the studied fishes. The ctenoid scale of A. jayakari was peripheral and characterized by the presence of one row of marginally located spines in two completed and uncompleted subtypes. The focus was positioned posteriorly or postero-centrally. The microscopic examinations revealed the presence of lepidonts of different sizes being very tiny, small, or prominent performing flat, blunt, pointed, short, or truncated shapes. The rostral margin of the scales was convex to moderately flattened and represented striate, scalloped, or waved types. Lateral fields were often flattened in all regions, while convex in the lateral fields of the scales of some individuals. The posterior field showed variations in different regions, for example, tapered and flattened ends. The anterior-posterior axis presented a laterally expanded or an elongated extension. The considerable morphological variation in the scales of various body regions makes it difficult to nominate a typical scale to be used in taxonomic studies. However, the key scales can be used for the comparison of different Awaous species.