There are nine named species of buckeye butterflies (genus Junonia Hübner) in the Western Hemisphere. There is considerable geographic variation within Junonia species, and possible ongoing hybridization between species, suggesting that Junonia may be a ring species, but also making this a very difficult group to define taxonomically. We tried to determine whether two forms of Junonia from Argentina – conventionally referred to as Junonia genoveva hilaris C. & R. Felder, the light buckeye butterfly, and Junonia evarete flirtea (Fabricius), the dark buckeye butterfly – were genetically distinct species or simply colour forms of a single species using morphological characters, mitochondrial cytochrome oxidase I (COI) DNA barcodes, nuclear wingless (wg) locus DNA sequences, and anonymous nuclear Randomly Amplified Fingerprints (RAF). Phylogenetic analysis of COI identified two distinct mitochondrial haplotypes that differ by about 4% sequence divergence; one confined to light‐coloured Junonia specimens and one shared between some light‐coloured Junonia and all of dark‐coloured Junonia specimens. Analysis of nuclear wingless sequences revealed 32 alleles among 22 Junonia specimens and showed significant genetic differentiation between light‐coloured and dark‐coloured Junonia. Analysis of RAF genotypes suggests that there are actually three genetically distinct Junonia populations in Argentina: two with light wing coloration, and one with dark wing coloration. Genetic evidence of recent hybridization among these populations was also observed, consistent with the ring species hypothesis. Careful comparisons of morphological characters between Argentinian Junonia and Junonia species from elsewhere in South America suggests that the two light‐coloured populations correspond to J. genoveva and either a genetically disparate population of the same species or an undescribed cryptic Junonia species, The dark‐coloured population may correspond to J. wahlbergi Brévignon. Our data suggest that COI DNA barcodes by themselves are not very useful for studying Junonia taxonomy, population structure or evolution.

Up to 9 described species of Junonia butterflies occur in the Americas, but authorities disagree due to species similarities, geographical and seasonal variability, and possible hybridization. In dispute is whether Caribbean Junonia are conspecific with South American species. Cytochrome oxidase I (COI) barcodes, wingless (wg) sequences, and Randomly Amplified Fingerprints (RAF) were studied to reveal Junonia population structure in French Guiana, Guadeloupe, Martinique, and Argentina. Phylogenetic analysis of COI recovered 2 haplotype groups, but most Junonia species can have either haplotype, so COI barcodes are ambiguous. Analysis of nuclear wingless alleles revealed geographic patterns but did not identify Junonia species. Nuclear RAF genotyping distinguished 11 populations of Junonia arranged into 3 clusters. Gene flow occurs within clusters but is limited between clusters. One cluster included all Argentinian samples. Two clusters included samples from French Guiana, Martinique, and Guadeloupe and appear to be divided by larval host plant use (Lamiales versus Scrophulariales). Many Junonia taxa were distributed across populations, possibly reflecting patterns of genetic exchange. We had difficulty distinguishing between the Caribbean forms J. zonalis and J. neildi, but we demonstrate that Caribbean Junonia are genetically distinct from South American J. evarete and J. genoveva, supporting the taxonomic hypothesis that they are heterospecific.