Epigenetic variation allows for rapid changes in phenotypes without alterations to nucleotide sequences. These epigenetic signatures may diverge over time among isolated populations. Epigenetic incompatibility following secondary contact between these populations could result in the evolution of reproductive isolating mechanisms. If epigenetic incompatibility drove the evolution of species isolating mechanisms, we expect to see significant epigenetic differentiation between these species. Alternatively, epigenetic variation could be the result of predominantly environmental variables and not align along species boundaries. A methylation sensitive amplified fragment length polymorphism analysis was performed on individuals of the closely related katydid speciesNeoconocephalusrobustusandN.bivocatus. We observed significant variation in total methylation levels between species. However, genetic differentiation remained larger than epigenetic differentiation between species groups. We measured a significant correlation between the epigenetic and genetic distance between individuals. Epigenetic differentiation is therefore likely the result of an interaction between genetic and epigenetic loci and not a mechanism for species differentiation. We therefore did not find evidence to support our hypothesis of an epigenetically mediated mechanism for speciation betweenN.robustusandN.bivocatus.