Officers raided a house on Dunstan Avenue around 9 p.m. Several other men and women were taken from the home and placed into police custody.
Moses, 27, faces numerous charges including one count of second-degree kidnapping, one count of assault by pointing a gun, one count of assault on a female, one count of communicating threats and failure to appear in court on earlier charges.
Police did not say if any of the charges against Moses are related to the Jadon Higganbothan and Antoinetta McKoy cases.
Sisk, 25, is charged with failure to appear in court on an earlier misdemeanor marijuana possession charge.
Moses is possibly a suspect in the death of 4-year-old Higganbothan, who was last seen in October 2010. A second missing person, 28-year-old McKoy, is also believed to be dead.
According to newly released court documents, Moses struck McKoy repeatedly over the last year with his hands and threatened to shoot and kill her if she left him.
A police informant also claims Moses killed Higganbothan and then ordered Sisk to kill McKoy.
ABC11 spoke with Jamiel Higganbothan, Jadon's father, Tuesday evening after he learned about the arrests.
Jamiel, who lives in Georgia, says the ordeal has been hard on his family.
"[There's] a little relief because they have the main suspects in custody," he said. "They're the only ones who know where my son is, where this young lady is ... it's hard on my family ... now that we have those two in custody, it's a big relief for everybody, but it still doesn't take away the pain."
Despite news of the arrests, Jamiel says it doesn't take away from the pain he feels having lost his son. Jamiel says the last time he saw his son was about two years ago, but now he knows why he didn't get to see him as often as he would have liked.
"It's hard to think of what could have happened to him and what could have been avoided," Higganbothan said.
Jadon and McKoy reportedly lived in a home with Sisk and several other women and children, who were members of a so-called cult known as the "Black Hebrew Israelites," before the group suddenly moved to Colorado.
Authorities have searched a Durham residence on Pear Tree Lane several times looking for evidence that could help them crack the case. Police searched a second home on So Hi Drive Monday in addition to a sewer system in the neighborhood. It is not known if anything was found.
Search warrants previously obtained by ABC11 from Colorado indicate that investigators believe the boy was killed possibly by Moses, who police believe is the leader of the group.
A new Durham search warrant made public last week says blood, a spent bullet, and shell casings were found at the home in a previous search. The warrant also states there were signs of "overt cleaning in the areas of the residence where these crimes were stated to have occurred."
While Durham police continue to maintain their investigation is a missing person's case, the warrant says "according to numerous witnesses ... Moses and Sisk were directly involved in the murder of a juvenile and an adult."
ABC11 asked Durham Police Chief Jose Lopez about the case at a news conference Tuesday -- hours before the arrests of Moses and Sisk. He said there was no information at that time to share with the public that could help crack the case.
No additional details were released about Tuesday's raid.
In the meantime, Moses is being held without bond, while Sisk's bond has been reduced to $2,000.