Both were also charged with 2nd degree felony child abuse and desecration of a body.
Both are eligible for the death penalty.
The aggravated murder charges carry possible mandatory penalties of death, life in prison without parole or 25 years to life in prison.
Prosecutors reserved the right under Utah to later file an intent to seek the death penalty against the Sloops.
Prosecutors have several days to submit such an intent.
Prosecutors said the decision regarding the death penalty will be made within the time allowed by law and that they will decide on an intent to seek the death penalty after they have received all relevant evidence and information and have carefully considered "...statutory, aggravating or mitigating circumstances."
Prosecutors also indicated that they will consult with the Utah attorney general's office, Layton Police and Ethan's family before filing such an intent.
The Sloops were arrested after the body of Ethan Stacy was found off a trail near Powder Mountain nearly 2 weeks ago.
A search was organized and later called off after continued police interrogation of the Sloops, who led investigators to a shallow grave near Powder Mountain. Ethan's body was recovered from the site and the Sloops were taken into police custody.
A Layton Police probable cause statement says Nathan beat Ethan and that the boy died in his bed after suffering from some sort of head trauma over several days.
The statement also indicated that the Sloops left Ethan locked in a bedroom at home on May 6th as the couple left home to get married.
Police say the Sloops left Ethan at home because they were afraid someone would notice the signs of physical abuse on the boy and turn them into authorities.
The Sloops were later arraigned in Farmington. A judge appointed both defendants new and separate counsel.
Tears rolled down Stephanie Sloop's cheeks as she appeared before the judge.
Nathan Sloop mouthed. "I love you," to his mother during the proceedings.
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