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Depends on who you think he should be with, it's up to the fans. Most likely Zelda because in spirit tracks they say Zelda from wind waker is Spirit Track's zelda's grandmothe, and she's in most games

In OoT, Link was infatuated with Zelda, as was stated in an interview - however, he was apparently the target of Navi's affection. In TP, Link expresses feelings for his childhood friend Ilia, and, like Navi, Midna was theorized to like him as well. In TWW, it's Tetra. Beedle hints at this, and it's pretty obvious, anyways. In Skyward Sword, the choice is obviously and undeniably Zelda. There are a few who suggest that Link liked Fi, or vice versa, but it's not even a valid theory. Fi was incapable of comprehending love and affection for the game's entirety, and Link's main target was Zelda. The Gift (talk) 04:49, September 14, 2012 (UTC)

Look at Timelinesplitter's blog: Relationships in the Zelda series here

Sort of related; That bit in TP with Link and Ilia, when he finds her in Telma's bar made me sad. :( 19:27, September 14, 2012 (UTC)