Climate change scenarios predict losses of cold-adapted species from insular locations, such as middle high mountains at temperate latitudes, where alpine habitats extend for a few hundred meters above the timberline. However, there are very few studies following the fates of such species in the currently warming climate. We compared transect monitoring data on an alpine butterfly, Erebia epiphron (Nymphalidae: Satyrinae) from summit elevations of two such alpine islands (above 1300 m) in the Jesenik Mts and Krkonose Mts, Czech Republic. We asked if population density, relative total population abundance and phenology recorded in the late 1990s (past) differs that recorded early in 2010s (present) and if the patterns are consistent in the two areas, which are separated by 150 km. We found that butterfly numbers recorded per transect walk decreased between the past and the present, but relative population abundances remained unchanged. This contradictory observation is due to an extension in the adult flight period, which currently begins ca 10 days earlier and lasts for longer, resulting in the same total abundances with less prominent peaks in abundance. We interpret this development as desynchronization of annual cohort development, which might be caused by milder winters with less predictable snow cover and more variable timing of larval diapause termination. Although both the Jesenik and Krkonose populations of E. epiphron are abundant enough to withstand such desynchronization, decreased synchronicity of annual cohort development may be detrimental for innumerable small populations of relic species in mountains across the globe.