We examined the distribution of submerged and emergent macrophyte species and the entire macrophyte community within and between five lake types (highland reservoirs, alkali lakes, large shallow lakes, small to medium sized shallow lakes, marshes) in the Pannon Ecoregion, Hungary. The lowest submerged, emergent and total species richness were found in alkali lakes. The highest submerged macrophyte richness was in small to medium sized lakes, while the highest emergent macrophyte species richness was in reservoirs, small to medium sized lakes, and marshes. The values of within-lake type beta diversity were generally lower than the values of alpha diversity, especially for submerged macrophytes, indicating between site homogeneity in species composition within the lake types. Emergent macrophyte communities contributed the most to within and between lake type diversity and total (gamma) diversity. Canonical correspondence analyses showed that the main environmental variables which influenced the distribution of submerged macrophytes were conductivity, Secchi transparency and water nitrogen contents. For emergent macrophytes conductivity, lake width, altitude and water depth proved to be the most influential variables. Our results contribute to the knowledge of large-scale distribution of macrophytes in the Pannon Ecoregion and to the identification of conservation value of lakes using macrophytes. The results support the importance of small lakes and artificial lakes in the conservation of macrophyte diversity compared to large and natural lakes in the Pannon Ecoregion.