Abstract Aim The main aim of this study was to compare different methods for the determination of both areas of endemism (AoEs) and biotic elements by analysing all the endemic plant species of a region, using our own data on the distribution of such taxa in the Maritime and Ligurian Alps. Our other goals were to use indicator species analysis (INDVAL) to identify and compare the species significantly associated with the AoEs detected by cluster analysis and parsimony analysis of endemicity (PAE), to compare these species with the results obtained by biotic element analysis, and to discuss the biogeographical meaning of the results obtained by all three methods. Location Maritime and Ligurian Alps, bordering north-western Italy and south-eastern France. Methods A presence/absence matrix of 36 endemic plant species was analysed using cluster analysis, PAE and biotic element analysis. INDVAL was used to compare the results obtained using these three methods. Results In an area such as the Maritime and Ligurian Alps, where the present distribution pattern of endemic taxa mainly reflects the influence of ecological factors, PAE and cluster analysis defined comparable AoEs characterized by the species that constituted the biotic elements. However, the biotic element analysis and AoE approaches revealed different relationships between the area/taxa congruence and the congruence among taxa ranges. Main conclusions The combined use of different methods seems to be useful for a complete description of the distribution patterns of taxa in a study area. INDVAL should be considered as a useful tool in biogeographical analysis for various reasons. It provides an objective criterion for dendrogram pruning based on the association rate between areas and taxon ranges. Because it identifies the strongest indicator species of each geographic unit, it allows comparison of the results of PAE and cluster analysis with those of biotic element analysis. Finally, INDVAL provides the rate of exclusivity and the rate of occupancy of each taxon in a given area.