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. This evidence concerns the gene CDH23 and deafness.