The Mediterranean area is regarded nowadays as one of the hot-spots of world biodiversity. The Baetic ranges in Spain have such a large number of endemic plant taxa that the territory has been recognized as a well-defined biogeographical unit. These endemic taxa tend to concentrate on disjunct highland areas that have been described consequently as ‘highland islands’. Despite the importance and complexity of these sites, the research carried out so far has produced only descriptive classifications. These approaches overlook the relationships between the sites and do not serve to identify the main centres of endemism. Herein, multivariate analysis techniques (cluster analysis and reciprocal averaging) and the parsimony analysis of endemicity (PAE), applied to the 222 orophilous endemic taxa of the Baetic ranges, have been used to reveal the floristic similarities between the areas involved, to identify the centres of endemism and to re-assess the previous classifications. Four centres of endemism are defined, one siliceous and three calcareous. The most outstanding feature in the Baetic ranges is precisely the floristic difference between siliceous and calcareous mountains. Calcareous territories extend along a SW–NE axis in line with the oceanic–continental gradient. The nature of the soil in the vast siliceous and calcareous–dolomitic territories of the Sierra Nevada is probably the cause of the remarkable floristic diversity. Not surprisingly, in our analysis these areas stand out as centres of endemism. We conclude that previous biogeographical classifications of the ranges are too rigid and do not properly reflect the floristic similarities of the area under study.