We investigated the auditory cortex (AC) to identify various subareas using transcranial flavoprotein fluorescence imaging in C57BL/6 mice. A single tonotopic map was observed in the low frequency area of the primary auditory cortex (AI). However, the high frequency area of AI was divided into two parts: the dorsal and the ventral high frequency areas. We performed SMI-32 immunohistostaining, and compared the staining patterns between the two high frequency areas and the low frequency area of AI. The staining pattern indicated that the ventral high frequency area and the low frequency area had similar patterns while the dorsal high frequency area may be different from other parts of AI. Precise analysis of tonotopic maps in AI showed that the map in AI was organized along the axis from the dorso-caudal parts to ventro-rostral parts of AI, while the dorsal high frequency area had an independent tonotopic axis from the ventro-caudal to the dorso-anterior direction. Moreover, AI was more plastic to tone exposure than the dorsal high frequency area. Two photon imaging revealed that the tonotopic map of AI was more homogenous in the dorsal high frequency area that that in other part of AI. Tracer injection into the dorsal high frequency area revealed that this area received inputs from a rostral part of ventral medial geniculate body, which does not project to AAF and other part of AI. These results strongly suggest that the dorsal high frequency area may be a distinct subarea in AC of mice. Male mice sing ultrasonic songs when they approach females, and females respond to the songs. We found some differences between female and male mice in the neural responses to ultrasonic male songs recorded in the dorsal high frequency area. The neural responses in female mice were larger than those in male mice, and were habituated in female but not in male mice. The latency to the male songs was shortest at the dorsal high frequency area. These results raise a hypothesis that the dorsal high frequency area in female mice might have some roles in perception of the male songs.