Background　Karst　tiankengs　serve　as　a　reservoir　of　biodiversity　in　the　degraded　karst　landscape　areas.　However,　the　microbial　diversity　of　karst　tiankengs　is　poorly　understood.　Here,　we　investigated　the　composition　and　function　of　the　microbial　community　in　a　karst　tiankeng.　Results　We　found　that　habitat　differences　inside　and　outside　the　karst　tiankeng　changed　the　composition　and　structure　of　the　soil　microbial　communities,　and　the　dominant　phyla　were　Proteobacteria,　Actinobacteria,　Chloroflexi　and　Acidobacteria.　The　Shannon-Wiener　diversity　of　microbial　communities　inside　and　outside　the　tiankeng　was　significantly　different,　and　it　was　higher　inside　the　tiankeng　(IT).　Venn　and　LEfSe　analysis　found　that　the　soil　microbial　communities　inside　the　tiankeng　had　640　more　endemic　species　and　39　more　biomarker　microbial　clades　than　those　identified　outside　of　the　tiankeng　(OT)..Functional　prediction　indicated　that　soil　microorganisms　in　outside　the　tiankeng　had　a　high　potential　for　carbohydrate　metabolism,　translation　and　amino　acid　metabolism.　There　were　biomarker　pathways　associated　with　several　of　human　diseases　at　both　IT　and　OT　sites.　Except　for　auxiliary　activities　(AA),　other　CAZy　classes　had　higher　abundance　at　IT　sites,　which　can　readily　convert　litter　and　fix　carbon　and　nitrogen,　thereby　supporting　the　development　of　underground　forests.　The　differences　in　microbial　communities　were　mainly　related　to　the　soil　water　content　and　soil　total　nitrogen.　Conclusions　Our　results　provide　a　metagenomic　overview　of　the　karst　tiankeng　system　and　provide　new　insights　into　habitat　conservation　and　biodiversity　restoration　in　the　area.