Several methods have been proposed for use in identifying and classifying areas of endemism. Parsimony analysis of endemicity (PAE) is the most widely used. It constructs cladograms based on the cladistic analysis of presence–absence data matrices of species and supraspecific taxa. Several authors have criticized PAE, usually because they have misunderstood its theoretical basis. A summary of the procedure is presented here, along with a discussion of the interpretation of PAE cladograms. Some critics deny any place in evolutionary biogeography for non-phylogenetic approaches, but I believe evolutionary biogeography is a pluralistic discipline, where PAE has a place despite lacking a strictly phylogenetic perspective, and thus can be applied as the first step in an analysis. Other authors criticize the use of PAE as a cladistic biogeographical method, although their arguments may be circular because they refer to biogeographical analyses based on phylogenetic hypotheses. Finally, the use of PAE for identifying areas of endemism has been criticized because an optimality criterion is used a posteriori to select areas of endemism found by what have been considered as less appropriate means, and endemicity analysis (EA) has proved to be more efficient than PAE for identifying areas of endemism. Over the last few decades PAE has been used extensively to identify areas of endemism and to determine their relationships, playing a relevant role in evolutionary biogeography.