Staff were told 65 jobs will go as part of a plan to cut the number by 200 by 2017.
Its stations, currently run separately, will be organised into two groups - one for pop music and one for classical and speech radio - and share some staff but keep their own controllers.
BBC Radio director Helen Boaden said the reorganisation was essential. She said: "BBC Radio is the envy of the world and our creativity is second to none.
"But we must also be as small as we can be, to meet our savings challenges and increase our agility in the digital world without losing our distinctiveness or damaging relationships with our many audiences.
"Reducing the division's head count by 15% is challenging, but shows how hard we are working to drive efficiency in everything we do."
The BBC said there were "no plans to change the way the stations are represented on-air".
Last week, Radio 1 announced it was axing long-serving presenters, including Edith Bowman and Rob Da Bank, as its boss admitted it had to make "tough choices" to cope with budget cuts.
Radio 1 controller Ben Cooper said the changes, which also affect 1Xtra, were in response to budget changes that were "hurting".