Background and aim Global warming is expected to have large impacts on high alpine and Arctic ecosystems in future. Here we report the effects of 18 years of experimental warming on two contrasting high alpine plant communities in subarctic Sweden.Methods Using open-top chambers (OTCs), we analysed the effects of long-term passive experimental warming on two high alpine plant communities, a species- and nutrient-poor heath and a more nutrient- and species-rich mesic meadow. We determined the impact on species composition, species diversity (at the level of rare, frequent and dominant species in each community), and phylogenetic and functional diversity.Key results Long-term warming drove differentiation in the species composition in both heath and meadow vegetation, with the warmed plots having distinctly different species composition in 2013 compared with 1995. In addition, variability in species composition increased in the meadow, while it decreased in the heath. The long-term warming had a significant negative effect on the three orders of phylogenetic Hill diversity in the meadow. There was a similar tendency in the heath, but only the phylogenetic diversity of dominant species was significantly affected. Long-term warming caused a reduction in graminoids in the heath, while deciduous shrubs increased. In the meadow, cushion-forming plants showed an increase in abundance from 2001 to 2013 in the warmed plots. Conclusions Responses in species and phylogenetic diversity to experimental warming varied over both time (medium vs long-term responses) and space (i.e. between the two neighbouring plant communities heath and meadow). The meadow community was more negatively affected in terms of species and phylogenetic diversity than the heath community. A potential driver for the changes in the meadow may be decreased soil moisture caused by the long-term warming.