The two accused, who have interim name suppression, appeared in the High Court at Timaru via audio-visual link this morning.
The 40-year-old and 32-year-old have also been charged with the serious assault and kidnapping of an Oamaru man last October.
The 32-year-old was also accused of possessing methamphetamine for supply.
The pair entered not guilty pleas to all of those charges.
Anaru Moana had been missing since last December.
Police were yet to locate his body.
The 37-year-old was reported missing on December 23, 2021 after last being seen at his mother's home in Waimate.
She had died only hours before Moana's disappearance.
In a statement last month, Detective Inspector Joel Syme said police had carried out an extensive search for the body of Moana, including searches of waterways in the Waitaki and Waimate areas.
While the search for Moana's body continued, Syme said he was pleased people were before the courts over his death.
"We hope that having two people charged with Anaru's death will give some comfort to the whānau, however, we know how important locating their loved one is, so this will remain a priority," he said.
The homicide investigation remained open and police continued to appeal for information on Moana's death and whereabouts, Syme said at the time.
The two accused would next appear before the court in February, when it was expected ongoing name suppression would be argued.
A trial was tentatively set down for July 2024.
