Zoom at his best (early appearances) would put up a good fight, maybe split 50/50. But over all Genis wins easily, he'd probably just tear every molecule of heat from Zoom's body and shatter him for the lulz.
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Besieged by countless foes, his eyes they are aglow, longing for the fight. He stands upon a mound, doesn't aim the throw, just lets the hammer fly!
Flash needed to steal speed from all the speedstes to hang with Zoom. Genis doesn't have that type of speed. Ever since that, Zoom has always been a beast.
Frankly speaking i dont care what version of zoom (hunter/thawne pre-52 or pre crisis or otherwise) is this because it doesn't matter. Throughout his history he's lost to flash a minimum of 8/9 times. Yes, he's always hyped up to be "far faster than before" and run circles around flash who then unleashes his full potential and beats him. Sometimes (though not always) with a bit of help but my point still stands. Hunter has also lost to lost to jesse-amped barry, regular barry even iirc. Let's not forget bart (albeit amped), wonder woman, or pied piper also beat him.
People also seem to forget that Genis has complete universal level cosmic awareness. He literally knows every single thing, it was explicitly stated that he knows every action and its consequences in the future so "surprising" him isn't going to work. The only time he had gaps in his CA is when there were space-time anomalies. He's also a borderline reality warper, having some minor space-time manipulation abilities. He should be able to handle zoom without much problems.
Moondragon stated that he could potentially be in tune with infinite multiverses and be all knowing (this was when his cosmic awareness was still in early development and experiencing problems with trying to harness it).
Reaffirmed when Magus tried to drain Genis' soul but it was too much for him to handle because he was effectively trying to drain the soul of reality itself.