Samuel Dieteman, 30, and Dale Hausner, 33, each face two counts of first-degree murder for the May 2 shooting of Claudia Gutierrez-Cruz and the July 30 shooting of Robin Blasnek.
They also are charged with 14 counts of attempted first-degree murder, 14 counts of aggravated assault and 16 counts of drive-by shooting.
"For many months our community has been terrorized by random killings and assaults," County Attorney Andrew Thomas said in a statement. "I am committed to an aggressive prosecution and will seek justice for the victims of these crimes."
Dieteman and Hausner are scheduled to be arraigned Aug. 21.
Police arrested the two men last week after keeping them under tight surveillance at an apartment they shared in a Phoenix suburb.
Sgt. Andy Hill, a police spokesman, said investigators are still trying to determine whether they are responsible for five more killings, three more nonfatal shootings and several animal shootings since May 2005.
"There is a lot of evidence to go through," Hill said Friday. "There is a possibility that another suspect or suspects may be identified down the road."
According to court documents, Dieteman and Hausner cruised around the city at night in a Toyota Camry, shooting at lone pedestrians and bicyclists.
Police hunted them for months, stymied by a lack of evidence at the scenes.
Defense lawyers could not be reached by telephone at their offices Friday for comment about the indictment.
Hausner's lawyer, Garrett Simpson, has asked a judge to move the case out of Maricopa County and place a gag order on authorities. He said media coverage will prevent Hausner from getting a fair trial.