In 2001, Troy Watkins was searching for his family's ancestral line. He learned that at FTDNA, he could start a project group and have others who shared the surname "Watkins" provide a DNA sample and compare the results to his and his cousin Pruett Watkins results. If the marker results matched for two or more members, then those that matched were, in fact, cousins, and have a common ancestor. Troy then became the first administrator of the Watkins project. Upon Troy's death, Linda Watkins, Pruett's daughter, took over the project.

New members who had yDNA that did not match Linda's branch were grouped into individual lines where they did have a match. Members of a subgroup line are able to exchange communications and family history data in their search for the common ancestor.