Research has challenged the idea that dogs already present in the Americas when Europeans arrived were swamped by animals brought in by the settlers.
The genetic study suggests modern breeds from the Americas largely trace their ancestry to dogs brought to the continent from Asia by native peoples.
It establishes a native Mexican origin for the popular Chihuahua - proposed by some to have recent roots in China.
Details appear in the Royal Society journal Proceedings B.
"Our results confirm that American dogs are a remaining part of the indigenous American culture, which underscores the importance of preserving these populations," he said.
Peter Savolainen, from the KTH Royal Institute of Technology in Stockholm, Sweden, and colleagues compared mitochondrial DNA from Asian and European dogs, ancient archaeological samples from the Americas, and American dog breeds.
These breeds included Chihuahuas, Peruvian hairless dogs and Arctic sled dogs.
They traced the American dogs' ancestries back to East Asian and Siberian dogs, and also found direct genetic links between ancient American dogs and modern breeds.
The ancestors of Native Americans crossed a land bridge linking north-east Asia and North America thousands of years ago. So a genetic link between dogs from these regions would be expected if they accompanied humans across the land bridge
Some dog enthusiasts had previously proposed a link between the Chihuahua and miniature dogs from China. But the latest research appears to rule that out.
"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."
The team also analysed stray dogs, confirming that these were generally runaway European dogs.
However, in Mexico and Bolivia, they identified populations with high proportions of indigenous canine ancestry.
Dr Savolainen said that the data also suggested the Carolina Dog, a stray dog population in the US, could also have a native American origin.
Sometimes referred to locally as the "yaller dog", it came to the attention of science in the 1970s, when I Lehr Brisbin, senior ecologist at the University of Georgia's Savannah River Ecology Lab, noticed its similarities to the Australian dingo.
The Carolina Dogs sampled in the study belonged to a branch of the dog genetic tree specific to East Asia.