Moores led Sussex to Championship glory in 2003 |
Moores, currently the National Cricket Academy director, will start on 1 May.
The appointment comes less than a day after Fletcher decided to step down after eight years in the role following England's exit from the World Cup.
"Peter has been identified for some time as a leading candidate as a future England head coach," said ECB chief executive David Collier.
The 44-year-old coached Sussex to their first County Championship title in 2003 and took charge of the National Academy in 2005.
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He has coached England A and worked with most of the current England team but has neither played nor managed a team at the highest level.
It was thought his main rivals for the job were Sri Lanka's Tom Moody, Bangladesh's Dav Whatmore and New Zealand's John Bracewell - who all have experience at the top level.
But Moores said: "It is an honour to have been appointed as head coach and to succeed Duncan, who has been an outstanding coach of the England team.
"I have enjoyed my two years at the National Academy and my role with the England teams.
"The challenge of this new role excites me and I look forward to meeting up with the players on their return to the United Kingdom and to leading England to success in both Test and one-day cricket."
Collier added: "The ECB has developed a contingency and succession plan for all key management positions and this is part of that.
"Peter is highly respected as an innovative and inspiring coach and is an ideal person to accept this appointment.
"In addition to the preparation of the Test team for the npower Test series versus the West Indies in four weeks' time, Peter will also commence the important work of preparing a new strategy for one-day cricket."
The appointment was backed by England captain Michael Vaughan, who said: "He's obviously got a great record at Sussex and he's done really well at the Academy. He's got a great enthusiasm for the game, he's forward-thinking and I really do think it's a great appointment for the English game.
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"He's got a great opportunity. The England team and the English game has got a lot of talent and we have to find the character and attitude to match that - but we have got a lot of talent to work with."
One player who could benefit from Moores's elevation is Sussex's wicket-keeper/batsman Matt Prior, who dismissed fears about his former coach's lack of international experience.
"His personality, enthusiasm for the game, and his ability to motivate individuals make him stand out," he told BBC Five Live.
"As for experience - look at what John Buchanan has achieved with Australia.
"It would be very easy to pin that on him but people should look at the positives he could bring to the England team."
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