Hybrid zones continue to provide unique opportunities for understanding fundamental ecological and evolutionary processes. In particular, when hybrid zones span sharp environmental gradients they provide insight into how a range of pure and admixed mammalian genomes interact with various ecological and environmental conditions. Here, we present our work on Neotoma lepida and Neotoma bryanti where these species meet and hybridise at a sharp ecotone between mesic foothill chaparral and Mohave desert scrub. Using genotype-by-sequencing approaches, we find that approximately 15% of the individuals across the ecotone are of hybrid origin, with pure parental types largely restricted to one of the habitat types. Because each taxon has access to different food plants in their respective habitat, and because woodrats are known to have locally specialised diets, we use high throughput sequencing of the trnL gene to gain insight into diet breadth in each habitat. The diet of each taxon is largely restricted to 1 or 2 plants that differ between the two habitat types. Further, the primary food plants used by each woodrat species are dominated by distinct toxic compounds that likely require different metabolic specialisations. We suggest that adaptation to different plant toxins may play an important role in determining species interactions at woodrat contact zones, providing a novel mammalian example of how ecological adaptation contributes to the maintenance of species boundaries.