This goes against the commonly held belief that the dogs present on the continent before European settlers arrived were swamped by the canines brought over.
Studies published in the Royal Society journal Proceedings B have revealed that many of America's dogs today were originally brought across by native settlers from Asia and have been almost completely preserved.
"Our results confirm that American dogs are a remaining part of the indigenous American culture, which underscores the importance of preserving these populations," said Peter Savolainen, a researcher in evolutionary genetics at KTH Royal Institute of Technology in Stockholm.
The Chihuahua, for example, was found to have Mexican origins, while it was recently thought to be from China.
"It was especially exciting to find that the Mexican breed, the Chihuahua, shared a DNA type uniquely with Mexican pre-Columbian samples," said Dr Savolainen.
"This gives conclusive evidence for the Mexican ancestry of the Chihuahua."
To reach these conclusions Dr Savolainen worked with colleagues in Portugal to compare mitochondrial DNA from Asian and European dogs, ancient American archaeological samples and modern American breeds such as the Chihuahua, Peruvian hairless dog and Arctic sled dogs.
The ancestry was found to go back to east Asia and dogs from Siberia, as well as show a connection between the ancient and modern breeds of American dogs.
These dogs would have been brought across to the Americas when the settlers crossed land bridge that linked North America to east Asia thousands of years ago.
They also looked at stray dogs in America and generally found that these were runaway European breeds, although many in Mexico and Bolivia are indigenous.
However, the Carolina Dog, a stray found in the US, is of native origin, forming a branch of the genetic tree found in east Asia.
Written by: Hannah