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Habitat heterogeneity can have considerable effects on gene flow and migration across a region of parapatry. Describing habitat across a region of parapatry is important for the development of eco-evolutionary theory. Two subspecies of thick-billed grasswren (Amytornis modestus) share a region of parapatry between the South Australian salt lakes, Lake Eyre and Lake Torrens. While the two subspecies remain morphologically diverged outside the region of parapatry, it is not known what factors within the region of parapatry may affect migration and gene flow. In this study, we test associations between habitat differences and subspecies distributions and discuss whether ecological barriers could play a role in mitigating gene flow between the subspecies. We compare dominant plant species (1) between the allopatric ranges of the subspecies and within their region of parapatry, and (2) in relation to presence or absence of grasswrens within their region of parapatry. We found that the dominant plant species differed between grasswren subspecies in their allopatric range and in their region of parapatry, and also differed in the region of parapatry at sites with or without grasswrens. Specifically, grasswrens were absent in vegetation that is typical of sand dunes. These findings are discussed in light of evidence for secondary contact and hybridisation between A. m. indulkanna and A. m. raglessi, and susceptibility to introgression.