They replace Steve Frost and Kath Beedles respectively.
Crowther, who is currently second-in-command at the Weatherfield soap, has worked her way up the ranks over six years and will join Steve Frost at the top in the New Year for a handover period before he vacates his office in March.
Speaking of her appointment, Crowther said: "From my time as series editor while Richard Hillman gripped the nation, through to the current meltdown of David Platt, Corrie has proved it does things differently, having the ability to move, amuse and excite its audience all at the same time.
"I'm looking forward to building on the show's recent successes while creating must-see storylines for 2008 and beyond."
She said: "Thirty-five years and Emmerdale is still fantastic. Being given the chance to help it go from strength to strength is such an honour - I can't wait."
Frost and Beedles will continue their work with ITV in "important new roles in the drama department". One of Beedles' first projects is said to be an Emmerdale spin-off which is due to begin production next year.
Both Kieran Roberts and Keith Richardson will retain their roles as executive producers for Coronation Street and Emmerdale respectively.
Director of ITV Productions John Whiston commented: "It's a time of change for the soaps. In the last couple of years under Steve and Kath and their teams, both soaps have defied gravity and held on to their massive audiences while all around were losing theirs.
"Both Steve and Kath are a terribly tough act to follow. That's why we are all thrilled that we've got Kim and Anita to step into their shoes. These jobs require passion, judgment, diplomacy, invention and, above all, superhuman stamina."
He added: "I'm also just as excited that we've persuaded Steve and Kath to stay within the company. We will be unleashing them soon into the wider drama arena where I know they will deliver great new shows for ITV Productions."