Some noticed the similarities and took to social media to criticise Nike over its use of the design.
The Gunas said in a statement that the company had not asked permission to use the design. Panamanian law recognises indigenous groups' rights to their intellectual property.
"We are not against our 'mola' being commercialised. What we oppose is it being done without consulting us first," said Belisario Lopez, the traditional leader of the Guna Yala community.
Lopez said the design represents "mother Earth, because the design is based on everything that is nature".
But, he noted the design "is a dress (style) exclusively for women".
A lawyer for the group said they didn't just want the shoe taken off the shelf. They also want compensation.
"There is already damage to our image, to our design, to our mola. We are not going to wait for it to be thrown away, we have to seek compensation," Aresio Valiente told a news conference in Panama City.