The matter was postponed to June 5 for further investigation, said spokeswoman Colonel Ronel Otto.
The teenager chose not to apply for bail at his last appearance. He is being kept in a place of safety, Otto said.
The 16-year-old was arrested at his guardian’s house in Mossel Bay, Western Cape.
He first appeared in the Mossel Bay Magistrate’s Court at the end of March.
Police said the matter was transferred to Mokopane because the bodies of the couple were discovered on their farm near Lephalale in Limpopo.
Police found the bodies of the 69-year-old man and 66-year-old woman after their relatives had been unable to contact them.