Conservation assessments of lichens have usually been based on scattered and methodologically diverse data. We illustrate the contribution of standardized inventories to conventional data sources by assessing the status of two conspicuous epixylic Cladonia species of conservation concern in Estonia. A time-limited inventory of all lichen species was carried out in 92 stands (2 ha each) in a balanced design of forests and clear-cuts. Cladonia parasitica (previously considered Regionally Extinct) was present in 13 stands with a total of 33 individual records, almost exclusively in dry boreal old-growth forests and clear-cuts. Thirty-six records of C. norvegica (previously six records) were made in 17 stands, most frequently in mature meso-eutrophic forests. On average, 1·5 hours of inventory were needed to discover C. parasitica in a stand, and 2 hours for C. norvegica. The scarcity of old records was probably due to the low local abundance of the species, their habitats being unpopular among lichenologists and expenditure of too short an inventory time in the field. Using habitat and frequency data, we estimate that the national population sizes of the species clearly exceed those set as IUCN criteria for species at risk. The key issue is the expected trend in substratum abundance, which suggests C. parasitica to be Near Threatened. We recommend stratified random sampling as an efficient method to collect quantitative information for lichen flora assessments.