Mr Hytner, who was appointed in 1994 by David Chance, the outgoing deputy managing director, is to become the marketing director of Channel 5, replacing David Brook.
BSkyB insiders say Mr Booth will now refashion the company's marketing, which has been responsible for much of the satellite broadcaster's success.
It is thought Mr Booth will focus less on sports as a driver for customers.
A spokesman for BSkyB confirmed Mr Hytner was leaving.
The spokesman added: "Mark has a clear strategy to accelerate the subscriber growth of the business.
"Sky's marketing will be key to that strategy."
Mr Hytner's exit comes just weeks after the resignation of Richard Brooke, who was the finance director.
Sam Chisholm, chief executive and managing director, has stepped down and Mr Chance is to leave in the new year, although he will retain a consultancy role with the company.