We analyze Yukawa unification in the the context of $E_8times E_8$ heterotic Calabi-Yau models which rely on breaking to a GUT theory via a non-flat gauge bundle and subsequent Wilson line breaking to the standard model. Our focus is on underlying GUT theories with gauge group $SU(5)$ or $SO(10)$. We provide a detailed analysis of the fact that, in contrast to traditional field theory GUTs, the underlying GUT symmetry of these models does not enforce Yukawa unification. Using this formalism, we present various scenarios where Yukawa unification can occur as a consequence of additional symmetries. These additional symmetries arise naturally in some heterotic constructions and we present an explicit heterotic line bundle model which realizes one of these scenarios.
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