This paper describes the present situation and problems in the conservation of native livestock breeds in Japan. The breeds considered include Japanese native horses, Japanese native cattle and Japanese native goats. To conserve the genetic resources of these breeds, it is important to keep them (1) in the form of live animals and (2) in the form of sperm, oocytes, embryos, cells, chromosomes and genes that can be stored by applying cryogenic techniques. For the Japanese native livestock that are also important members of living ‘museums’, it may be further desirable to conserve them as live animals. However, it is difficult to conserve all these breeds in a living form due to their low economic value in the market. Therefore, it is necessary to keep these animals for other purposes such as riding horses, tourist attractions in national parks and zoos, educational tools in agricultural schools and experimental animals.