"For years, varied and sometimes wild claims have been made about the origins of a group of dark-skinned Appalachian residents once known derisively as the Melungeons. Some speculated they were descended from Portuguese explorers, or perhaps from Turkish slaves or Gypsies.
"Now a new DNA study in the Journal of Genetic Genealogy attempts to separate truth from oral tradition and wishful thinking. The study found the truth to be somewhat less exotic: Genetic evidence shows that the families historically called Melungeons are the offspring of sub-Saharan African men and white women of northern or central European origin."
Last year Roberta Estes, et al. published a peer reviewed paper in the Journal of Genetic Genealogy (http://www.dnaexplain.com/Publications/PDFs/MelungeonsMulti-EthnicP...)
"Many people expected to discover that the Melungeons were primarily Native American, but this was not the outcome of the DNA project. In fact, many of the direct paternal male lines were African and all of the direct maternal female lines tested were European."
That study is once again in the news, DNA testing continues to show that the Melungeons are an African / Anglo mix, with very little Native American and no identifiable Portuguese.
Jack Goins (co-author of the study) did a detailed review of the available records recently. This is a apparently the first time anyone has looked at the entire set of records rather than focusing on single lines. Goins concludes, "The written land, tax, census and court records agrees [sic] with the DNA results."
Roberta Estes explains more about the records:
Bottom line: the ongoing research continues to show that the Melungeons are neither Indian nor Portuguese. Basically, those were just ways to explain away being a little darker than the neighbors.
This 2012 article explains more about the results of the DNA study, as well as reasons early Americans denied any links to an African heritage.