Global warming is expected to have large impacts on high alpine and Arctic ecosystems in the future. Here we report effects of 18 years of experimental warming on two contrasting high alpine plant communities in subarctic Sweden. Using open-top chambers, we analysed effects of long-term passive experimental warming on a heath and a meadow. We determined the impact on species composition, species diversity (at the level of rare, common and dominant species), and phylogenetic and functional diversity. Long-term warming drove differentiation in species composition in both communities; warmed plots, but not control plots, had distinctly different species composition in 2013 compared with 1995. Beta diversity increased in the meadow, while it decreased in the heath. Long-term warming had significant negative effects on the three orders of phylogenetic Hill diversity in the meadow. There was a similar tendency in the heath, but only phylogenetic diversity of dominant species was significantly affected. Long-term warming caused reductions in forbs in the heath, while evergreen shrubs increased. In the meadow, deciduous and evergreen shrubs showed increased abundance from 2001 to 2013 in warmed plots. Responses in species and phylogenetic diversity to experimental warming varied over both time (medium (7 years) vs long-term (18 years)) and space (between two neighbouring plant communities). 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 long-term warming. © 2021