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DNA ploidy levels were estimated using DAPI‐flow cytometry of silica‐dried specimens of the European mountain plant Senecio carniolicus (Asteraceae), covering its entire distribution area in the Eastern Alps (77 populations, 380 individuals) and the Carpathians (five populations, 22 individuals). A complex pattern of ploidy level variation (2x, 4x, 5x, 6x, and 7x cytotypes) was found in this species, which has been considered uniformly hexaploid. Hexaploids predominated in the Eastern Alps and was the only cytotype found in the Carpathians, while odd ploidy levels (5x, 7x) constituted a small fraction of the samples (<1.3%). Tetraploids occurred in two disjunct areas, which correspond with putative Pleistocene refugia for silicicolous alpine plants. Diploids occurred in large portions of the Alps but were absent from areas most extensively glaciated in the past. Intrapopulational cytotype mixture was detected in 22 …