It is well known that animals can exert strong selective pressures on plant traits. However, studies on the evolutionary consequences of plant–animal interactions have mainly focused on understanding how these interactions shape trait means, while overlooking its potential direct effect on the variability among structures within a plant (e.g. flowers and fruits). The degree of within-plant variability can have strong fitness effects but few studies have evaluated its role as a potential target of selection. Here we reanalysed data on Ipomoea wolcottiana stigma–anther distance to test alternate mechanisms driving selection on the mean as well as on intra-individual variance in 2 years. We found strong negative selection acting on intra-individual variation but not on mean stigma–anther distance, suggesting independent direct selection on the latter. Our result suggests that intra-individual variance has the potential to be an important target of selection in nature, and that ignoring it could lead to the wrong characterisation of the selection regime. We highlight the need for future studies to consider patterns of selection on the mean as well as on intra-individual variance if we want to understand the full extent of plant–animal interactions as an evolutionary force in nature.