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Green was in front of a judge Thursday for a hearing on a motion for his release.
Last week a judge ruled that the jury had been denied information that would have compromised the prosecution's key witness and threw out Green's conviction.
The witness, Willie Finley, recently recanted his trial testimony, saying he was high on cocaine during the killing and had been helped by police to identify Green as a suspect.
With prosecutors opting not to seek a retrial, Marcus today ordered that Green be set free.
Green was greeted by his attorneys and supporters as he walked out of a criminal court building in downtown following a hearing Thursday.
"First I would like to thank God. I am humble to be here in front of all of you today. I would like to thank all of the people who believed in me, my wife Mary and my son especially. I use to feel bad that my wife had to travel to see me. I knew that this day would come. I never asked for mercy. I only asked for justice and it was served today. I would like to thank the District Attorney's office, even though they put me in here I am not bitter. I do not hate anybody. I am a better man today. I graduated from college. I teach school. I teach men. The men in San Quentin believe in me. I would like to thank the media for being here today. If you didn't believe in me you wouldn't be here, thank you," said Green.
Mary Green credited her faith with helping her and her husband persevere over the past two decades.
"Well, it was nothing but, you know, a lot of love and it took a lot of time," she said. "And one thing that we did is we put God first and our marriage second. And with that, you know, we were able to overcome all the obstacles."
The Los Angeles County district attorney's office said Wednesday it would not oppose his release.
Eyewitness News reporter Leo Stallworth and The Associated Press contributed to this report.