Falklands veteran Admiral Sir Philip Jones took over the command of 30,000 men and women, as well as nearly 90 warships and vessels.
Admiral Sir George Zambellas stepped down after commanding the country's sea defences for three years.
Admiral Jones began his career in the Royal Navy in 1978.
He said: "In these uncertain times, the Royal Navy continues to protect our nation's interests at home and around the world.
"In the years ahead, the introduction of the two largest aircraft carriers in our history will change the Royal Navy entirely."
Admiral Zambellas said: "It has been an enormous honour to lead the Royal Navy.
"It has a fantastic future ahead of them, as they grow their Navy's capability and ambition. If I could, I'd join it all over again."
The Royal Navy currently faces a shortage of 500 sailors, resulting in two warships being docked in Portsmouth for six months to speed up the training of new recruits.
The leadership of the Royal Navy has formally changed in a ceremony on board HMS Victory in Portsmouth.