Although the designation of traditional protection areas has an aggressive purpose of protecting biodiversity, it often deprives the rights of living of aboriginal peoples and results in environmental injustice. In this regard, the designation of protection areas is a double-sided sword. On the one hand, it is an important tool for achieving biodiversity; on the other, it has become a powerful tool of damaging environmental justice. Therefore, what kinds of approaches and mechanism should be adopted to designate protection areas and to preserve biodiversity has become one of the major issues regarding the management of protection areas. This study uses literature review to examine the context of biodiversity and environmental justice and attempts to search for common principles in these two seemingly contradictory perspectives. Further, this study adopts these principles to evaluate the Tanayiku, Chiayi County. The accomplishment of biodiversity and environmental justice is a process of paradigm shift. Moreover, by adopting empowerment to help implement the sharing of powers and by learning processes to achieve symbiosis of human and the nature are necessary foundations for effectively managing protection areas and the necessary requirement for achieving sustainable development. From the Tanayiku experience, this study proposes two important apocalypses: paradigm shift and empowerment. Based on these two apocalypses, three operational strategies are suggested: monitoring and evaluation, participatory management, and appropriate development.