Fish scales are an important structure used as a versatile research material. Research on fish scales from the point of view of ichthyological has unique characteristics for each fish species. This research aims to reveal the surface variations of the Dorsal Scale microstructure of three fish species from the Chaetodontidae family, namely Chaetodon Auriga, Chaetodon kleinii, and Chelmonrostratusin support of fishery resources conservation efforts. Research on reef fish families is still very minimal in Indonesia. On the other hand, this reef fish family is very massive in exploitation. This is the important reason for researching fish scales from the Chaetodontidae family. In the research on the microstructure of fish scales, the focus is more on the components of fish scales. The method used in this research involves extracting scales from Chaetodon Auriga, Chaetodon kleinii, and Chelmonrostratus. The results of this microstructural analysis using Transmission Electron Microscopy (TEM) and Scanning Electron Microscope (SEM) with a magnification of 65-15,000 times are evidence that can reveal differences between species, and genera of fish in the Chaetodontidae family. The results of this research indicate that three types of Butterflyfish from the Chaetodontidae family have different morphological forms (oval, rectangular, and elliptical), ctenii, lepiddont, and focus. In Chelmonrostratus no focus was found. This research concludes that the character of three types of Butterflyfish on the Dorsal Scale can show the characteristics of the scales which are evidence of identification for the taxonomic process of the Chaetodontidae family in addition to molecular.