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We explored the fine-scale distribution of cytotypes of the mountain plant Senecio carniolicus along an altitudinal transect in the Eastern Alps. Cytotypes showed a statistically significant altitudinal segregation with diploids exclusively found in the upper part of the transect, whereas diploids and hexaploids co-occurred in the lower range. Analysis of accompanying plant assemblages revealed significant differences between cytotypes along the entire transect but not within the lower part only, where both cytotypes co-occur. This suggests the presence of ecological differentiation between cytotypes with the diploid possessing the broader ecological niche. No tetraploids were detected, indicating the presence of strong crossing barriers.