Hybrid zone models often consider environment-independent selection to operate against all hybrids. However, empirical studies suggest that hybrids may be as fit or fitter than the hybridizing parental taxa in some environments. In this study we develop a novel mathematical model to explore the effects of one form of hybrid superiority on the genetic structure of hybrid zones. Our primary goals were to investigate the allele frequency clines at a locus experiencing overdominant selection and at a linked neutral or underdominant locus. Our results indicate that overdominant selection results in flat equilibrium allele frequency clines throughout the hybrid zone and an excess of heterozygosity relative to Hardy-Weinberg equilibrium. However, the genetic clines at linked neutral or underdominant loci tend not to reflect this overdominance even when the loci are tightly linked. Overall, we conclude that overdominance is unlikely to be detected in genetic surveys unless many loci are assayed.