Calcareous and rich fens harbour the unique biodiversity of plants and invertebrates. They are extremely sensitive to landscape changes because of their island nature. In the Carpathians, they are still well-preserved, but their number has substantially decreased. Knowledge about their variability and classification into vegetation units, a baseline for efficient nature conservancy, is still insufficient in the Eastern Carpathians, where phytosociology has used different methodologies than in the Western Carpathians. It has resulted in artificial boundaries in the distribution of vegetation types and low compatibility with modern European habitat classification schemes. Here we gathered a large set of vegetation-plot records, sampled by the unified sampling protocol. The aim was to uncover the principal variation in compositional data, identify resulting clusters with the hitherto reported vegetation units, and create the unified classification system adjusted for the entire Carpathian territory. In line with previous ecological studies, the unsupervised classifications (Twinspan, beta-flexible clustering method) largely mirrored the base saturation gradient and distinguished between relict fens and younger fen grasslands. We defined formally the cores of 10 vegetation units well reproduced by unsupervised classifications and used them as prototypes in semi-supervised k-means clustering. The final 10 clusters essentially correspond with phytosociological associations, with five of them being reported for the first time for Romania. These vegetation units were well-separated in the principal coordinate analysis, whose first axis separated relict fens from younger fen grasslands, while the second axis followed the water level gradient largely. Groundwater pH and conductivity contributed to forming significant compositional gradients. Climate (temperature, precipitation, number of hot days above 30°C) and specific edaphic conditions contributed to the diversification of the vegetation types. Our analyses supported the classification of fen grasslands into both the tufa-forming and the peatforming ones, belonging to different associations and Habitat Directive units, both occurring in all countries including Romania, rather than having a single separate Eastern-Carpathian association. We provide strong evidence for distinguishing the Sphagno warnstorfii-Tomentypnetalia order and its alliances Sphagno warnstorfii-Tomentypnion nitentis, Stygio-Caricion limosae and Saxifrago hirculi-Tomentypnion in Romania, the latter missing in other Carpathian countries. The final unified classification system will make Carpathian vegetation types of rich and calcareous fens applicable to continental habitat classification schemes.