Present-day intraspecific diversity has largely been shaped by previous climatic events, but the spatial and temporal scales of differentiation processes in most species remain to be clarified. In Europe, the Pleistocene glacial cycles have generated population structures that remain especially evident in montane taxa. The intraspecific variation of the European subalpine Yellow-spotted Ringlet, Erebia manto (Denis & Schiffermüller, ), shows a hierarchical, two-level structure that allows us to study intermediate stages of speciation. Morphologically, three subspecies clusters have been described in this butterfly: the manto, bubas- tis and vogesiaca type. An allozyme study previously revealed two genetic lineages within the manto type, and two within the vogesiaca type, but lacked bubastis representatives. To further our knowledge of the intra- specific structure of E. manto, we sampled all known and presumed intraspecific groups and sequenced 1,496 base pairs of the mitochondrial gene COI for 152 specimens from 15 localities. A median joining haplotype network, based on 40 parsimony informative sites, confirmed the four allozyme based lineages. The bubastis type was acknowledged as a fifth genetic lineage, replacing the manto type populations in the southern part of the western Alps, and separated from it by a well-known zoogeographic borderline. We discuss how the present-day distributions, genetic relationships and timing of the differentiations align.