Mires or peatlands host unique biodiversity and provide many valuable ecosystem services. Mires often undergo different development phases during their evolution. Two mire phases that have clearly divergent hydrological regimes and characteristic biotas are minerotrophic fen and ombrotrophic bog. Open mires can be overgrown by trees and develop into peatland forests. Mire development trajectories are expected to be associated with three major factors—post‐glacial isostatic uplift, autogenic succession and climate‐induced changes. Understanding long‐term mire development is important for the conservation planning of these threatened habitats. We use data from modern pollen samples to characterize differences between the pollen signal and to identify indicator pollen taxa for three mire development phases—open fens, forested fens and bogs. The modern reference samples are then used to support the interpretation of the sediment records in terms of mire development phases and related biodiversity changes in six mires within a 20 × 30 km area in western Saaremaa, Estonia. Palynological richness and phylogenetic diversity (PD) as well as Ellenberg indicator values are compared throughout the 10,000‐year history of the Saaremaa mires. Pollen of herbaceous taxa discriminates between open fens, forested fens and bogs, and indicator pollen taxa can be associated with each mire phase. In general, the fen phases of the mires show higher richness and PD than the bog phases but there is considerable variation between the sites. The mire diversity peaks are often associated with transitional periods when high local community heterogeneity allows the coexistence of high numbers of taxa from different phylogenetic lineages. Synthesis. When the initiation of mires in isostatic land uplift areas is closely related to water‐level changes and the position of the sites in relation to the sea, the development of mires and their biodiversity in the late Holocene is associated with local conditions but mediated by climate. The ongoing rapid climate change is likely to accelerate changes in existing mires, and while the transitional periods are characterized by high diversity, these periods are temporary, and the overall diversity of mires can be expected to decrease. When the initiation of mires in isostatic land uplift areas is closely related to water‐level changes and the position of the sites in relation to the sea, the development of mires and their biodiversity in the late Holocene is associated with local conditions but mediated by climate. The ongoing rapid climate change is likely to accelerate changes in existing mires, and while the transitional periods are characterized by high diversity, these periods are temporary, and the overall diversity of mires can be expected to decrease.