Altitude lakes are weakly impacted by human activities. This makes them choice ecosystems to understand how biological communities are impacted by natural factors. This question was addressed to littoral benthic diatoms, a largely used ecological indicator. We wanted to know if benthic diatoms in lakes are more impacted by local varying factors (altitude, lake depth...) or regional varying factors (geology). The study area takes place in the Northern French Alps. Littoral benthic diatoms of 63 natural lakes situated between 1350 and 2700 m · a.s.l. were sampled. Two categories of communities were observed: one of deep and lower altitude lakes and one of higher altitude and shallower lakes. In each category, communities were characterized and were corresponding to particular lake types: lakes dominated by a particular geology, lakes with a water level fluctuation, turbid lakes,... Communities did not show a spatial structure. We observed that local factors were more important than regional factors. Indeed, the study area displayed a mixed geology even at a local level. On another hand, altitude a local varying factor determines freezing period a determining item of high-altitude lake functioning.