Yaku sika deer (Cervus nippon yakushimae) are endemic to Yakushima Island, whose landscape covered with primary evergreen forest is recognized as a World Heritage Site. In this study, the rumen bacterial microbiota (RBM) of wild Yaku sika was characterized using high throughput sequencing of bacterial 16S rRNA genes combined with targeted cultivation and functional analyses. Comparative analyses of RBM datasets from other ruminant animals revealed distinct community structure among domesticated and wild ruminants. Wild Yaku sika RBM exhibited higher species richness than other sika deer (i.e. wild Ezo sika and domesticated sika deer), likely reflecting their dietary variations associated with unique ecosystem in the island. The Yaku sika RBM of high deer population density samples exhibited higher diversity and contained higher proportion of Firmicutes than those of lower density samples. Moreover, the highest abundance of tannase gene were observed in individuals from the highest population density area, consistent with the previous observation that Yaku sika in the high density areas expanded their feed to include tannin-rich unpalatable plants. This study indicated that RBM of unique wild Yaku sika contribute to the flexibility of dietary shift and thus maintaining nutritional status of Yaku sika under high density conditions.