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Microhabitat choice plays a major role in shaping local patterns of biodiversity. In butterflies, stratification in flight height has an important role in maintaining community diversity. Despite its presumed importance, the role of behavioural shifts in early stages of speciation in response to differences in habitat structure is yet to be established. Here, we investigated variation in flight height behaviour in two closely related Heliconius species, H. erato cyrbia and H. himera, which produce viable hybrids but are isolated across an environmental gradient, spanning lowland wet forest to high-altitude scrub forest. Speciation in this pair is associated with strong assortative mating, but ecological isolation and local adaptation are also considered essential for complete reproductive isolation. We quantified differences in flight height and forest structure across the environmental gradient and tested the importance of resource distribution in explaining flight behaviour. We then used common garden experiments to test whether differences in flight height reflect individual responses to resource distribution or genetically determined shifts in foraging behaviour. We found that the two species fly at different heights in the wild, and demonstrated that this can be explained by differences in the vertical distribution of plant resources. In both the wild and captivity, H. himera choose to fly lower and feed at lower positions, closely mirroring differences in resource availability in the wild. Given expectations that foraging efficiency contributes to survival and reproductive success, we suggest that foraging behaviour may reflect local adaptation to divergent forest structures. Our results highlight the potential role of habitat-dependent divergence in behaviour during the early stages of speciation., (© 2022 British Ecological Society.)