The calcareous forests in northern Europe are characterised by a very high species diversity including numerous red-listed species. The aims of the current study were: (i) to describe the Estonian calcareous forests' diversity both on the species and community levels, (ii) to identify the indicator/characteristic species of the established community types and, (iii) to identify the main environmental factors affecting these communities. Of the 271 recorded vascular plant species, 55 occurred in such forests within their geographical distribution limit or close to it. Regarding soil properties, the humus-horizon C content, CaCO₃ content and loss on ignition (LOI) were found to affect the total number of species. All in all, 12 community types were established, each having their own dominating and statistically reliable indicator species. The community types also differed in their structure and characteristics of the soils (particularly humus horizon thickness and depth of the rubble layer). Although calcareous forests are rather threatened, in Estonia they still grow in relatively large and non-fragmented areas.