Few convenient/expeditious methods for identifying the species of shed snake skins in specific areas have been developed. The scales on shed snake skins are permeable to light and can be examined by light microscopy (LM), which is of higher availability—especially for wild animal researchers and citizen scientists—than conventional approach which examines the scale microstructures by scanning electron microscopy. We collected and examined a total of 801 shed samples or scale specimens from 53 snake species in Taiwan and adjacent islands, and developed the first guide to identify the fragmented or faded shed skins of most snake species by LM. Morphological characters of scales can be examined by LM include the apical notch, apical pits, apical lobes, keels, scale symmetry, unpigmented spots (mechanoreceptor-like organs), interscale follicles, cross/longitudinal micro-ridge, oberhautchen cells, rows of spines, light/tiny dots, and other microstructures. The microstructures on the scale specimens prepared by the stripped method and the impression method were similar to those on shed skins when examined by LM. We investigated the variations of scale morphology associated with ontogeny, body region, and position on scales, discussed the character evolution of snake scale morphology, and certified that the interscale follicles and the unpigmented spots could also be useful characters for shed skin identification. The methods and results of this study could be applied to identify squamate skins/sloughs and even fecal remnants.