The animals were pinched from Bruno’s near Daventry late last month, police said.
Store manager Jackie Hunt told the Northampton Chronicle the thief removed the tortoises from a locked vivarium then put them in his pockets.
Police confirmed the thief “concealed” his booty “in his trousers” and appealed for witnesses.
“We saw the CCTV later and it clearly showed the man bending down and breaking the lock, before taking out the tortoises,” Mrs Hunt told the BBC.
“He was wearing jogging bottoms and he put one in each pocket.”
Their micro-chips are registered on the tortoises’ licences, which are still held by the pet shop, meaning they cannot legally be owned in this country.
The theft happened at the shop in Whilton Locks Garden Village at about 16:00 on 25 April.