<p>High-mountain species are particularly vulnerable to the effects of climate change, such as warming, drying, and isolation. While the role of temperature and hydroperiod in structuring communities along an altitudinal and connectivity gradients has been demonstrated in high-mountain lakes or rivers, very few studies have been conducted in high-mountain ponds, and the role of hydroperiod and network connectivity remains actively debated. To understand which environmental factors structure high-mountain pond communities, we investigated the relationship between three biotic groups (Odonata, Amphibia, and macrophytes) and their environment in 500 ponds in the French Alps and Pyrenees. As predicted, most communities varied along an altitudinal gradient, though not uniformly across all the alpine biogeographic regions studied. We also showed that water permanence is a key determinant of community variation in high-mountain ponds common to all the geographic zones studied. Finally, we demonstrated that connectivity between ponds should be maintained to conserve high-mountain Odonata specialist communities and mediate the effects of temperature and water permanence in the context of climate change. In order to design effective conservation measures for high-mountain pond communities, further research is needed on the drought resistance of non-permanent pond communities and on their dispersal potential between high-mountain ponds.</p>