Peruvian wildlife authorities found 29 small tortoises - two of them dead - in a cardboard box on a bus on its way from northern Peru to Lima.
Officials made the discovery while working to identify a suspected international wildlife trafficking ring, which has a route from Peru to the European black market.
The driver and transportation company are under investigation.
As the tortoises are small, Galapagos park officials said genetic studies will be necessary to determine the zone of the archipelago they were taken from.
The Pacific island chain off the coast of Ecuador is famous for its unique flora and fauna studied by Charles Darwin as he developed his theory of evolution.
Lonesome George, the last known member of the subspecies Geochelone nigra abingdoni, died in 2012.
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