Galápagos tortoises are a symbolic animal in terms of conservation biology as well as evolutionary biology, and both in situ and ex situ conservation programs are currently underway. For endangered species, captive individuals can perform a certain role as genetic reservoirs for ongoing and future breeding programs We examined the genetic identities of two giant tortoises in Ueno Zoo, Japan. The mitochondrial genotype of the older tortoise, Taro, as appeared to be that of Chelonoidis porteri from Santa Cruz island. The mitochondrial genotype of the younger tortoise, Kamekichi, was identified as either C. becki from the northern area of Isabela island, or C. darwini from Santiago island. These genetic analyses serve as reference data for the future conservation management of captive Galápagos tortoises.