He was found dead at his home in Dunmow, Essex, this morning.
Police are not treating the death as suspicious.
An Essex Police spokesman said: “We were called to concerns for the welfare of a man at an address in Brook Hill, North End, just after 8.10am on Monday
“We attended and, sadly, a 49-year-old man was pronounced dead at the scene. His next of kin have been informed.
“The death is not being treated as suspicious and a file will be prepared for the coroner.”
Tributes are pouring in for the iconic frontman from the world of music.
Ed Simons from The Chemical Brothers wrote on Twiitter: "Oh gosh, so sad to hear about Keith Flint, he was always great fun to be around and very kind to Tom and I when we first started doing shows together..great man."
The Black Madonna said: "RIP Keith Flint. I damn near burned a hole through The Prodigy Experience in 92 when there wasn't a lot of accessible dance music in Kentucky. It was a huge deal for me. I can't overstate it. I'm very grateful to have had proof that this world I wanted so badly actually existed."
Update: Keith Flint's death has been confirmed as suicide.
Samaritans is a charity that aims to help people suffering emotional distress. They are free to contact 24/7 from any UK or Irish phone by dialling 116 123. Head to samaritans.org for further details.
Patrick Hinton is Mixmag's Digital Features Editor, follow him on Twitter
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Our tribute to Keith Flint