We analyzed the hair microstructure of Korean small terrestrial mammals, such as Rodentia and Lagomorpha, to classify the characteristics of hair morphology. Micromys minutus showed a unicellular irregular type of medulla structures; on the other hand, the other mammals showed multicellular structures. Regarding the cuticular scale structures, the Rodentia species exhibited a narrow and broad diamond petal type, while the Lagomorpha species exhibited an elongated petal type. Interestingly, the hair cross-sections showed quite unique characteristics. We constructed hair identification keys to distinguish species with a single hair. The dichotomous key of Rodentia and Lagomorpha can be used for their behavioral ecology and dietary analysis of upper predators to serve as the basis for ecological research.