The normal and lateral line scales from above the head and four flank regions were investigated in two goatfishes by using light microscopy to evaluate the microscopic characteristics of scale surface ornamentation from different body parts of these fishes and to add new morphological data for their discrimination. The body scales were removed and digital images captured with a Dino‐Lite digital camera connected to a Leica compound microscope. The presence of both transverse and longitudinal radii was a distinctive characteristic for the scales of studied goatfishes. The most distinctive features of the key scales discriminating the two goatfishes were the scale shape, the presence of irregular grooves in scale surface, the presence of transverse radii in the lateral fields, and the availability of lepidont at the anterior field. The lateral line scale ornamentations were almost similar in two species; however, the lateral line canal was branching in Parupeneus heptacanthus. Scale extension index indicated that in both species, the dimension of normal key scales tends to the right, while the dimension of lateral line scales tends to the left. This study accentuated that scales from different body regions may exhibit variation in surface ornamentations, that scale morphology could successfully be used to discriminate the examined goatfishes, and that the use of fish scale microscopy is an easy and relatively rapid method and does not require fish sacrifice. Since fish identification is essential for the conservation and management of species, the use of scale morphology to this purpose appears particularly promising.

Macro‐ and microscopic characteristics of flank scales for 12 species were investigated from the Persian Gulf Coral Reefs. In Lutjanus argentimaculatus and L. russellii (family Lutjanidae), the scales of different flank regions were not different, while four characters showed variation in the scale of L. lutjanus i.e., scale shape (pentagonal, hexagonal and square), anterior margin (waved, scalloped and smooth), focus shape (circular and oblong) and focus position (postero‐central and central), displayed variation. Scale type (ctenoid) and posterior margin (transforming ctenii) did not show variation and could be considered to be specific in this family. In Epinephelus chlorostigma (family Serranidae), the scales of flank regions did not display variation, while in E. areolatus, E. diacanthus and E. radiates, the scales showed considerable variation. The most variable characters were scale shape, posterior margin and focus shape. Therefore, in fish systematics studies on the base of scale, it is particularly important to compare scales from the same flank regions. Also, some criteria such as size‐dependent alternation, ontogenetic changes and variation between flank regions, should be considered. This study supports the potential of scale morphology to help for the understanding of fish diversity in the coral reef ecosystem.