"What's unusual and unique about the site is that it's this huge chunk of land where a major part of this ancient Tequesta village site is preserved," archaeologist Bob Carr told The Miami Herald.
The site is "one of the earliest urban plans in eastern North America. You can actually see this extraordinary configuration of these buildings and structures," Carr said.
The Tequesta settlement was located at the mouth of the Miami River in what today is the heart of downtown Miami.
The discovery has created a problem for city officials and MDM Development Group, which plans to build a movie theatre, restaurants and a hotel on the site.
Florida and Miami-Dade County preservation officials want the city to look at other options for the site in an effort to save all or part of the archaeological zone.
Archaeologists, who have been digging at the site for months, have discovered eight large circles with holes that may have been the foundations of Tequesta dwellings.
The team led by Carr, who works for the developer, found an Indian burial ground under the third phase of the project, where a Whole Foods market, parking garage and residential building are under construction.
The site's historical importance is magnified by the fact that Fort Dallas, a 19th-century US Army post, and the Royal Palm Hotel, built by oil and railroad tycoon Henry M. Flagler, were later built over the Indian village.
Archaeologists have found thousands of items at the site, such as bones and tools used by the Tequestas.