The 13-part series will begin shooting in Wales and Morocco in April, while BBC controller of drama Ben Stephenson confirmed that it will air on BBC One in Merlin's Saturday night slot this autumn.
The series synopsis states: "The city of Atlantis is a mysterious, ancient place; a world of bull leaping, of snake haired goddesses and of palaces so vast it was said they were built by giants.
"It's into this strange, compelling realm that the young Jason arrives and an amazing adventure begins, bringing to life the vast store of Greek myths and legends re-imagined for a new generation."
Other commissions include Death Comes To Pemberley, a three-part adaptation of PD James's homage to Jane Austen's Pride and Prejudice, written by Juliette Towhidi (Calendar Girls).
Set six years after Pride & Prejudice ends, the show centres around a murder mystery plot involving Elizabeth Bennet and Mr Darcy.
Breakdown is an eight-part thriller written by Jack Williams and Harry Williams, about a man whose son is snatched while on holiday in France.
The Interceptor is another eight-part series from Tony Saint, telling the story of a top secret law enforcement team aiming to hunt down Britain's most dangerous and ruthless criminals.
Emma Frost's Jamaica Inn is a three-part adaptation of the classic Daphne du Maurier novel, a gothic romance set in 1820 and centred around young Mary Yellan, who becomes entangled in a dangerous criminal world.
Remember Me is a three-part mystery from Gwyneth Hughes, about a frail old Yorkshireman who becomes the sole witness to a violent death while moving into residential care.
BBC Two has also announced the second and third parts of David Hare's MI5 trilogy, which began with Page Eight in 2011, titled Turks and Caicos and Salting the Battlefield.