The agricultural landscape of central Europe has changed dramatically in recent decades due to intensified cultivation, bringing many of its characteristic species to the brink of extinction. We investigated whether landscape structure affects the genetic structure and diversity of remnant populations of the two arable plant species Adonis aestivalis and Consolida regalis. We used dominant amplified fragment length polymorphism markers (AFLPs) and compared populations from six regions of 5 km² in central Germany. These regions represent two different classes of landscape structural complexity: intensively used, homogeneous landscapes (>95% of area covered by arable land with low extent of field margins) or heterogeneous regions (<60% of area covered by arable land with large extent of field margins). Contrary to expectations, within-population diversity levels did not significantly differ between homogeneous and heterogeneous landscapes. No significant isolation-by-distance was found for either species, regardless of landscape structure, and genetic structures may still mirror more continuous conditions before large-scale restructuring commenced in Germany's arable landscapes from the 1950s onwards. These results suggest that current landscape complexity, as such, is not as important for local-level genetic structure for the species studied. Thus, homogenised and intensively used landscapes may also be important for the conservation of arable plant diversity and should not be neglected.