Sheikh Mohammed is to merge his global racing and breeding operations under the Godolphin banner.
John Ferguson, the sheikh's long-time bloodstock advisor, will be the chief executive and racing manager of Godolphin.
Darley, under which all Sheikh Mohammed's bloodstock holdings formerly operated, is now to be used solely as a brand to promote stallions.
His new role means Ferguson will hand in his licence as a jumps trainer at the end of April to devote himself to Godolphin.
"It is an exciting new chapter in the Godolphin story. Our long-term objective is to improve on Godolphin's results on the racetrack," Ferguson said.
"I will miss the training. Jump racing has always been one of my sporting passions, and I love the involvement.
"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," he said.
Godolphin has 2000 horses in training in Britain, Ireland, Australia, the United States and Dubai while Darley stands stallions around the world.