By performing the differential expression and alternative splicing analyses on the transcriptomes of cochlea in four Rhinolophus taxa, we identified some DEGs or ASGs related to hearing loss or deafness in human or mice (e.g., OTOS, CEACAM16, LRP2, and CDH23), and these genes might be associated with sexual difference of echolocation pulses in bats. Here, CDH23 is linked to hearing loss disorder.