Magistrate Eddie Hall issued the warrant for Zwelithini Maphanga, who was arrested along with Tshepo Malambe and Mike Mkansi on suspicion of illegally hunting a rhino in the Kruger National Park in 2011.
Malambe and Mkansi were present in court on Thursday.
Maphanga’s lawyer told the court he did not know his client’s whereabouts.
Hall said: “During the previous court appearance, Mkansi was not present. It seems the accused are taking turns being absent.
“Maphanga’s bail amount will now be forfeited to the State and a warrant for his arrest will be issued.”
Malambe was remanded in custody while Mkansi’s bail was extended with a warning that he appear again on September 16.
In a separate case in the same court, three suspected poachers also appeared on charges of illegally hunting a rhino.
Sifiso Lephoko, David Mawelele, and Daniel Dlamini were arrested in the Stoltznek section of the park in March 2011.
Prosecutor Isabet Erwee told the court that Dlamini and Mawelele were currently serving time for other crimes while Lephoko was on bail.
The matter was postponed to September 16.
In a third case, Jonas Makhubela, who was arrested for illegal hunting in the park early this year, told the court he was prepared to plead guilty.
Hall told him a legal aid lawyer has been appointed to help him with his plea bargain.
“Your attorney will assist you in the procedure to be followed and you should tell him everything you need the court to know regarding your case.”
The case was postponed to September 5 for the defence to prepare the confession statement.