Caves gives an insight into the life forms and geological formations below the Earth’s surface. Karstic environments are one of the most diverse geomorphological occurrences. Speleothem, secondary mineral deposits, are one of the important characteristics of a karst caves. In this work microbial communities present in Leye caves in the Vezere valley in Dordogne, France that will be acceded by High-throughput sequencing (HTS). In situ Dino Lite analyses allows us to examine the existence of microorganisms. In vitro culture confirmed the presence of bacteria, fungi and yeast and high throughput sequencing approaches allowed us to explore, compare and characterise the microbial communities in different parts of the cave. Bacterial community are mainly composed by Proteobacteria, Actinobacteria and Firmicutes, but Phylum like Nitrospirae, Tenericutes or Spirochaetes are also presents in the cave. The study gives important contribution to assess the microbial communities present in limestone caves.