John Ferguson, currently sitting in fifth place in the National Hunt trainers' championship, is to relinquish his licence in April to take up a new role with Godolphin.
Ferguson has made a real success of taking Godolphin horses from the Flat and turning them into jumpers, but due to Sheikh Mohammed's decision to amalgamate the Darley breeding operation and Godolphin's racing arm as part of a "streamlined" business, that will now come to an end.
Long-standing bloodstock advisor to Sheikh Mohammed, Ferguson is to become chief executive and racing manager.
The best of Ferguson's horses will join Charlie Appleby, with Ferguson's staff at Bloomfields in Newmarket also offered the chance to join Godolphin.
However, Appleby was quick to stress he would not be taking out a dual licence.
"I won't be training any jumpers," said Appleby.
"There'll be no dual licence, what will happen is the best of John's horses will come back to race on the Flat, some of them still have pretty lofty ratings.
"It will be nice to add some four- and five-year-olds to our string as we have a lot of younger horses at Moulton Paddocks, we haven't had the older ones before.
"It's exciting to have those type of horses and it will give us a nice balance."
Ferguson began training in 2011-12 and nearly struck at the Cheltenham Festival in his first season when New Year's Eve finished second in the Champion Bumper.
He has two Grade One wins to his name, those of Ruacana in the Finale Hurdle at Chepstow in 2013 and Parlour Games in the Challow Hurdle at Newbury last year.
The news can be viewed as a blow to Aidan Coleman, who was appointed Ferguson's retained jockey in July.
"I am extremely proud of the team at Bloomfields and the excellent job they have done over the past five years," Ferguson told www.godolphin.com.
"They are a fantastic group who have given everything to the stable and I am very grateful for their hard work.
"It is an exciting new chapter in the Godolphin story. Our long-term objective is to improve on Godolphin's results on the racetrack.
"I feel honoured to be appointed chief executive and racing manager, but I realise that it will require more of my time and attention.
"I will miss the training. Jumps racing has always been one of my sporting passions, and I love the involvement.
"I am very grateful to Sheikh Mohammed for giving me the horses to send jumping in the first place.
"In fact, he wanted me to continue, but I could see that Godolphin must always be a priority and requires my undivided attention.
"It makes sense for the racing and breeding operations to merge. One is sourcing the other, and a well-planned, common strategy can only strengthen both.
"We must ensure that Godolphin continues to represent excellence in racing, and that the brand serves as a constant reminder of the vibrancy and energy of Dubai."