Wilson has overseen Ko's rapid rise to the top of the women's game, coaching the prodigy for 11 highly-successful years after meeting a five-year-old Ko at Pupeke Golf Course in 2002.
"It's been an honour to help develop Lydia into the number four golfer in the world," Wilson said in a statement. "When I first met her the golf clubs were taller than she was and she didn't know the first thing about a driver or a putter but now she has one of the most envied swings in the women's golf world.
"We've spent a lot of time together over the past decade and during that time I've become very close to Lydia and her family. While I'm incredibly disappointed that our 11 year partnership is over, I respect Lydia and her team's decision."
The timing of the announcement comes a week after Ko signed a management and marketing contract with sporting giants IMG. Newstalk ZB reported Ko has agreed to be coached by well known American David Leadbetter when she is in the United States.
Ko won five pro titles while being coached by Wilson, four of which came as an amateur before the 16-year-old turned professional in October.
"Lydia's consistent and outstanding performance is the ultimate payback for any coach and it has been truly wonderful working with someone with her talent, dedication and focus," Wilson said.
"I wish Lydia all the best and will watch proudly as she embarks on what I'm sure will be a hugely successful professional golfing career."
