Gouffre de la Sambuy is an alpine cave, located in the French northern Western Alps, in the Bauges massif. This subalpine massif is included in the "delphinohelvetic" domain of the external Alps, drifted over the foreland (jurassian and molassic domains). Bauges massif presents with these folded structures a medium altitude (< 2 500 m asl) and mountainous relief built with only sedimentary rocks. To the east of the massif, the Sambuy summit is 2198 m asl, the main entrance of the cave (SB9) is open at 1 820 m asl. The average of temperature in this area is 1.6°C. The precipitations are over 2 100 mm/year. The cave is approximately 900 m development and 120m depth. The final part of the cave is on the top of the Hauterivian marls. During speleogenesis studies on 2012, speleologists have founded bacterial mats and gypsum in the marly parts of the cave. Upper, in the middle part, the Barremian limestone wall of a 25 m shaft was covered by unusual fine and white deposits looking like lichen. To understand these ecosystems, climate aerologic measurements like air temperature, pressure, and wind speed were realized during each visit in winter, spring and summer. Due to the difficulties to access to the cave with no possibilities to get electrical power, no monitoring was realized for the climate parameters. In spring, the wall deposits have been sampled with swab and store in sterile tube for laboratory molecular analysis. DNA was extracted, PCR amplifications and cloning-sequencing were performed targeting bacterial 16SrRNA and eukaryotic 18SrRNA genes. For the bacterial community, we identified 29 different OTUs and the richness estimator (Schao) showed a global richness of 65 OTUs. The bacterial community was mainly composed by Proteobacteria, Acidobacteria, Actinobacteria, Nitrospirae and an important part of uncultured bacteria. Some of these bacterial taxa are known to be involved in nitrogen cycling. For the eukaryotic community, 32 OTUs were identified from our clones library, and the Schao index showed a global richness of 86 OTUs. Rhizaria (with mostly Cercozoa, genus Cermononas) was a dominant group, followed by Fungi (mostly Dikaria). Some Alveolata belonging to Ciliophora were also detected, as well as an important part of uncultured fungi and others. Additional sequencing analyses should be performed to depict in depth the taxonomic composition in these microbial mats. Our preliminary results showed that these microbial mats comprised a rather high diversity of prokaryotic and eukaryotic taxa, which physiological/biochemical characteristics and biotic interactions have still to be described.