The actor will appear opposite Lily Collins in the adaptation of Cassandra Clare's young adult fantasy novel, according to The Hollywood Reporter.
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The tale follows the adventures of Clary Fray (Collins), a young woman who discovers that she is a Shadowhunter - the descendent of half-angel warriors who protect the world from demons.
Rhys Meyers will play powerful and crazed Shadowhunter Valentine Morgenstern, who seeks to purify the world at any cost.
The Harald Zwart-directed film will also feature Lena Headey, Jared Harris and Kevin Zegers.
Best known for his starring role in The Tudors, Rhys Meyers also appeared in Mission: Impossible 3.
He will next be seen in NBC's new Dracula television series.
Filming on The Mortal Instruments: City of Bones will begin in Toronto in August.
