Jon Amiel will direct, and the cast will also feature Jeremy Northam, Toby Jones and Benedict Cumberbatch.
The film is not described as a traditional biopic, instead as 'part ghost story, part psychological thriller, part heart-wrenching love story.' The story focuses on Darwin's years as a young man whose adored 10-year-old daughter Annie helps him battle his demons and reconnect with his family.
The young actress playing Annie will be announced soon.
The film, formerly known by the working title of Nature, will be directed by Amiel (Entrapment) from a screenplay by John Collee (Master And Commander) based on Randal Keynes' book Annie's Box.
Thomas' Recorded Picture Company will produce and sister company HanWay Films is handling worldwide sales. The project was co-developed with BBC Films and the UK Film Council. Icon Film Distribution has already come on board for UK and Australian theatrical rights.
Shooting starts Sept 28 on locations including Darwin's own home, Down House. The film is being readied for a 2009 release to coincide with the bi-centennial of Darwin's birth.
The Origin Of The Species author's life is seen as a collage of scenes from past and present, laced with images of exotic animals and the dark dreams of Darwin's troubled mind.
'John Collee's compelling script tells the remarkable story behind Darwin's revolutionary theory and the foundation of a book that changed the world. We think of Darwin as an old man with a grey beard, the reality of our story is very different,' said Thomas.
Jamie Laurenson, executive producer, BBC Films, added: 'BBC Films are delighted that such a great cast is in place to bring to life John Collee's fantastic script. We are very pleased to be working with Jon Amiel and Jeremy Thomas' RPC on what we are sure will be an emotionally powerful and important film.'
HanWay's slate also includes TIFF titles Genova and Of Time And The City, plus Sam Taylor Wood's forthcoming John Lennon biopic Nowhere Boy and Gerald McMorrow's Franklyn.