The news of break-up comes after Deschanel was photographed cosying up to a new man last month on the set of her upcoming film 'Rock the Kasbah', reported Us magazine quoting multiple sources.
The actress was spotted again with the man, who has since been identified as Jacob Pechenik, a producer on her latest film.
Deschanel, 34, and Linden began dating back in June 2012, shortly after her split from ex-husband Ben Gibbard, the lead vocalist of 'Death Cab for Cutie'.