Melissa Hack, Ross Hack and Leland Jones were charged with murder and firearms offenses in the deaths of Daniel Shersty and Lin Newborn, who belonged to a group that fought against racism.
Butler was convicted of murder in 2000 and is serving two consecutive life sentences in state prison.
The Justice Department said evidence at Butler's trial indicated that the defendants were affiliated or associated with racist neo-Nazi skinhead groups at the time of the killings. Newborn and Shersty were members of the Anti-Racist Action Group, also known as the Skinheads Against Racial Prejudice.
"This case demonstrates that the Department of Justice will be vigilant in working to ensure that every perpetrator of racially motivated violence is brought to justice," Assistant Attorney General for the Civil Rights Division Thomas Perez said Wednesday in a statement.
Ross Hack and Melissa Hack face potential penalties of life in prison or the death penalty. Jones, who was not yet 18 at the time of the killings, faces up to life in prison, the Justice Department said.
The Los Angeles Times said Melissa Hack was Butler's girlfriend at the time of the shootings. During Butler's trial, prosecutors alleged Hack and another woman lured Newborn and Shersty to the desert site where the shootings occurred, the newspaper said. Newborn was black and Shersty was white.