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“Genetic resources” means something of biological origin with utility value. Genetic resources have been used by countries since ancient times as the foundation of numerous industries, including agriculture, medicine, food, and chemicals. In this respect, Japan is no exception; the active collection, preservation, and utilization of genetic resources is occurring in various fields of endeavor. Genetic resources were traditionally considered to be the common property of all humankind. However, in 1993, when the Convention on Biological Diversity came into force, it was recognized that a country’s sovereign rights extended to owning genetic resources. In 2010, Japan chaired the 10th meeting of the Conference of the Parties to the Convention on Biological Diversity(COP10) and the Nagoya Protocol was adopted. Japan is now preparing to ratify this protocol. The objective of the Nagoya Protocol is to enable practical ways to share the benefits accruing from the use of genetic resources. Upon implementation of the protocol, the acquisition and use of genetic resources is expected to change significantly. Against this backdrop, this paper briefly reviews the current state of genetic resource usage and the challenges ahead for the preservation and use of Japan’s genetic resources. We take examples from the fields of agriculture, microorganisms, academic disciplines, and marine genetic resources, with a particular focus on extraterritorial preservation (preservation outside the genetic resourceﾕs natural habitat).