Macaronesia was recognized as a biogeographical region more than a century ago. However, this concept has been recently criticized due to the floristic heterogeneity of the region. This paper analyzes and interprets the inter-island floristic similarities using presence-absence data for 30 islands and 3114 phanerogamous species. Agglomerative classification, method UPGMA, and Principal Coordinates Analysis were applied. The results show a close correlation between variation in floristic similarities and latitude, altitude and distance from the continent. These correlations are interpreted in relation to the variation in climatic conditions, the possibility of long -distance dispersion and island size. We conclude that the selective effect of climate and opportunity for long-distance dispersion are the primary factors explaining the present inter-island floristic variation.