Opened in July 2004, founding members in the Center mostly came from College of Bioresources and Agriculture. Successive directors, including Professor Ping-shih Yang (楊平世) and Professor Cheng-jen Shih (石正人) from Department of Entomology, planned and participated in local biodiversity research by Council of Indigenous Peoples. Since October 2012, incumbent Director / Associate Professor Yuan-chao Tung (童元昭) from Department of Anthropology focuses on expanding discussions on contemporary indigenous issues and supporting strong environments for indigenous cultural development.

With new website, Facebook page and YouTube channel in May 2013, the Center aims to broadcast information and facilitate conversations on indigenous issues from various perspectives. This is helpful to enrich and expand understandings to indigenous issues, and constitute a society with cultural diversity.