In Japan, geographic variation in bird song is known only on small peripheral islands with isolated populations, and has not been reported in any species on the main islands of Japan, probably due to the close proximity of the populations on the relatively small main islands. On Honshu, one of the four main islands of Japan, the Yellow Bunting Emberiza sulphurata breeds in restricted habitats (i.e. wet grasslands with forest edge, or wet grasslands with sparse forest). This may facilitate the isolation of its populations and may have led to geographic variation in its songs. We investigated the acoustic characteristics of the songs of Yellow Buntings from four populations in central Honshu and found differences among the populations. For example, males at Nagaoka sang short songs with highly frequency-modulated notes, whereas males at Fuji sang long songs with poorly modulated notes. This study demonstrated geographic variation in bird songs on a small scale in mainland Japan. As songs are formed through cultural learning, local songs can arise in loose isolation or for short periods.