Much of the existing genetic research has been done on European populations, but scientists say differing genetic make-up can be vital in understanding the prevalence of diseases and how to treat them.
For example, "in lung disease, such as asthma or emphysema, we know that it matters what ancestry you have at specific locations on your genes," said Esteban Gonzalez Burchard, bioengineering professor at the University of California, San Francisco and one of the study's senior authors.
The research, out Thursday online in the US journal Science, analyzed nearly a million genetic variants among more than 1,000 people from different ethnic groups within Mexico.
Around half of the subjects came from 20 different indigenous populations, while the other half were of mixed African, European, and Mexican descent.
They found that some of the indigenous groups differed as much from each other as Europeans do from east Asians.
The results confirmed that "for disease classification, it also matters what type of Native American ancestry you have," said Burchard.
"In terms of genetics, it's the difference between a neighborhood and a precise street address," he explained.
Doctors have long used ethnic heritage as a guide for certain diagnoses, such as in estimating baseline lung capacity measurements, crucial for determining if a person's lungs have later been damaged by disease or environmental factors.
But categories as broad as "Latino" or "African American" can be misleading and result in misdiagnoses.
In this study, "not only were we able to measure... diversity across the country, but we identified tremendous genetic diversity, with real disease implications based on where, precisely, your ancestors are from in Mexico," said first author Christopher Gignoux, now a postdoctoral fellow at Stanford.
Researchers focused on Mexico because the country includes a large variety of indigenous groups dating back to the days before Christopher Columbus first brought Europeans to the Americas.
The study found significant differences in lung capacity among different ethnic groups -- with mixed-race Mexicans and Mexicans with western indigenous ancestry on one side, and Mexicans with eastern indigenous ancestry on the other.
According to the data, a healthy Mexican from the west of the country would, in terms of lung function, appear up to 10 years younger than a counterpart from the Yucatan peninsula, in Mexico's southeast.
"This can shape public health and public policy," said Burchard of the findings.
"We now have a map of Mexico that will help researchers make those clinical and public health decisions."