I speculate that the heart belongs to Graham. I highly doubt the idea that it’s a heart of a Storybrooke citizen from a gruesome murder.
From what I understand, the hearts that the Queen collects are still beating when she stores them away – but seeing how Emma & Ruby didn’t pass out from seeing beating heart in the mysterious box by the bridge, I assume it was life-less. I wonder if part of the magic of her storage unit is to keep the hearts alive- so in order to ensure the death of Graham, Regina had to find a new hiding place for his heart. It would make for quite a confusing discovery if DNA test reveal that it belongs to someone who’s still alive – the results would just be ignored as a mistake. However, if they came back as a match with Graham, things would get much more interesting and give the characters cause for discovering who they really are.
As a last note, I believe Mary-Maragret’s fingerprints on the box came from FairyTale Land, not Storybrooke.