Historically, morphological variation has been used to classify many species (and subspecies) of Lepidoptera. However, some of this variation may be unsuitable for inferring the recent evolutionary history of populations. Genetic data provide an alternative. We examine the morphological and genetic variation within and between British subspecies of Coenonympha tullia (Müller 1764) to test the hypothesis that neutral genetic variation corresponds to morphological variation. We find that most morphological and genetic variation occurs within populations and that those populations designated as subspecies based on morphological characters are not necessarily most closely related for mitochondrial DNA or nuclear DNA (amplified fragment length polymorphisms and allozymes). Thus, the notion that wing spot variation reflects population isolation and therefore genetic differentiation does not hold. The present study highlights the need for genetic data where taxonomy may be based on environmentally plastic or locally adapted characters because such characters will not reflect the true population genetic history. © 2009 The Linnean Society of London, Biological Journal of the Linnean Society, 2009, 97, 314–327.