High altitude rivers in European mountains show a large diversity of benthic diatom assemblages. Diatoms were studied from rivers of the Alps, the Pyrenees, the Massif-Central and the Iberic system. The study area spread across four countries, Italy, France, Switzerland and Spain. Since 2000, the European Water Framework Directive (WFD) has required the assessment of stream quality using bioindicators and any deviation from reference conditions measured. References for each river type and for each bioindicator, such as diatoms, are in the process of being defined.System A is a typological system proposed by the WFD, in which ecoregions spread over several countries were defined. The first aim of this study was to assess the importance of these ecoregions for diatoms compared to other environmental factors. To reduce the heterogeneity of the diatom assemblages due to the river continuum and also pollution, only the rivers higher than 800 meters were selected. These rivers include a majority of sites that are only slightly polluted, or not at all. In total 261 sampling sites were considered from four ecoregions: the Iberic region, the Pyrenees, the Alps and the Western Highlands. The sampling sites were characterized by differences in geology, distance from the source and altitudes. Statistical analysis showed that geographic ecoregions of system A and geology were the most important environmental descriptors for diatoms. Distance from the source and altitude were less important and pollution was the least important parameter.The second aim was to describe and to typify the main diatom assemblages of these European mountains. Eight clusters gathered into four main groups were identified. Group I was mainly recorded in the Alps and the Pyrenees; group II had in common its close proximity to the source; group III was often found in the Western Highlands on crystalline geology, and group IV was present in all ecoregions and included weakly polluted streams. Some suggestions for the improvement of the ecoregions based on benthic diatoms were given in the conclusion.