After two decades operation of the initial environmental specimen banking, a new program, Environmental Time Capsule Program, started in 2002 as a government-supported long-term program to construct a firm scientific basis for various environmental research studies. The program consists of long-term environmental specimen banking activity and specimen collection of endangered wildlife and is based on cryogenic sample preservation facility called Environmental Time Capsule building, which completed construction in 2004. After 9 years of extensive research, research focuses have been selected and the program was reorganized to the environmental sample collection part and endangered wildlife collection part in 2011. Due to huge environmental disaster caused by the Great East Japan earthquake and the tsunami as well as subsequent nuclear power plant accident at Fukushima, a new sampling and monitoring program started at affected areas in collaboration with the reorganized environmental sample collection and archiving program. Outlines of the quality assurance and quality control (QA/QC) activities in the program and future perspective under related international activities, particularly Stockholm Convention, are reported.