Dale Hausner, 33, and Samuel Dieteman, 30, entered their pleas via a video link during a brief hearing.
Each is charged with two counts of first-degree murder and 14 counts of attempted murder. The two former roommates also pleaded not guilty to 14 counts of aggravated assault and 16 counts of drive-by shooting in connection with the 16 victims.
Their attorneys declined to comment after the hearing.
Policethe two men in early August after keeping them under tight surveillance at an apartment they shared in a Phoenix suburb.
At a news conference announcing the arrests, authorities said they were confident they had the right suspects.
"These are the two monsters we have been hunting, and I promise you and our colleagues promise you, we are not finished," Phoenix Mayor Phil Gordon said.
Hausner and Dieteman are being investigated in a total of 37 shooting incidents stretching back to May 2005. Seven people were killed during the shooting series and 17 wounded. Several animals also were shot.
A task force is still searching for another serial predator, dubbed the "Baseline Killer," who has been forensically linked to eight killings and several robberies. Police also believe he is responsible for 11 sexual assaults on women and young girls.