Sika deer Cervus nippon populations have been increasing on the Japanese archipelago. Their range is expanding to include the alpine zone in central Japan, where they stay during summer before descending to the lower areas during winter. No studies on dietary habits of alpine deer in mainland Japan have been conducted. This study assessed the composition of sika deer diets and compared nutritional quality between the low montane, subalpine and alpine zones. We analyzed sika deer fecal samples from Mt Yatsugatake (YT) and the Japanese South Alps (SA). In the lower mountain in YT, dwarf bamboo comprised 40–55% of the plant compositions in fecal samples, whereas dicots were mostly found in SA samples. In subalpine zones in YT, grasses are an important food item, comprising about 50% of the samples. In SA, monocots (10–20%) and dicots (10–20%) were both prevalent. In the alpine zone of both YT and SA, grasses were present the fecal samples (50% and 10–20%, respectively). Crude protein contents were higher at higher zones (15–20%) than at lower zones (8–12%) in both study areas.