The auditory system of the Korean greater horseshoe bat (Rhinolophus ferrumequinum korai, RFK) is adapted to its own echolocation signal, which consist of constant frequency (CF) element and frequency modulated (FM) element. In contrast, the Japanese long-fingered bat (Miniopterus schreibersii fuliginosus, MSF) emits FM signals. In the present study, the characteristics of stereocilia in RFK (a CF/FM bat) and MSF (a FM bat) were studied in the apical turn of the cochlea where the lower frequencies are transduced. Stereocilia lengths and numbers were quantitatively measured in RFK by scanning electron microscopy and compared with those of MSF. Each inner hair cells (IHCs) of RFK possessed three rows of stereocilia, whereas MSF possessed five rows of stereocilia. Gradients in stereocilia lengths and numbers of stereocilia of the IHCs of RFK were found to be less pronounced and fewer, respectively, than those of MSF. Each outer hair cells (OHCs) possessed three rows of stereocilia in both species. OHCs stereocilia in RFK that distinguished it from MSF were a shorter length and a greater number of stereocilia. These features suggest that the apical cochleas of RFK are adapted for the processing of higher frequency echolocation calls rather than that of MSF.