Male Bengalese finches have a complex song-sequence pattern containing multiple elements. Learning and producing songs require memorization of the phonology and the sequence of elements. We tested the auditory memory of male finches for their own songs to determine whether the auditory memory included the sequence of elements. An immediate early gene ZENK is induced by auditory processing in the secondary auditory area of the caudomedial nidopallium (NCM) and the caudomedial mesopallium (CMM) in response to song presentations. Repeated presentations of the same song result in a decrease in ZENK expression in these areas, reflecting habituation to auditory processing. We examined sequential differences in auditory processing using the habituation-dishabituation method. After repeatedly presenting the male finches' own song stimulus, we changed the stimulus to a shuffled sequence of songs. If the shuffled songs induced ZENK expression, it indicated that the auditory areas had been dishabituated by the sequential differences. The shuffled songs caused intermediate ZENK expression in the NCM when compared with the expression by a conspecific new song and that by the same song. The tendency toward intermediate expression was similar in the CMM; however, a significant difference was observed between the conspecific song and shuffled songs. These results suggest that the sequential difference caused a partial dishabituation in the NCM. Thus, the auditory areas processed not only the phonology but also the sequence of songs.