Karst　tiankeng　are　important　biodiversity　conservation　reservoirs.　However,　the　unique　habitats　of　karst　tiankeng　affect　microbial　community　structure　remained　poorly　understood.　In　this　study,　we　collected　soil　samples　from　karst　tiankeng　(TK)　and　karst　land　(KL)　and　subjected　to　high-throughput　sequencing.　Based　on　the　classification　of　the　total,　abundance,　and　rare　taxa　for　bacteria　and　fungi,　a　multivariate　statistical　analysis　was　carried　out.　The　results　revealed　that　bacterial　community　Shannon　diversity　and　Pielou’s　evenness　were　highest　in　TK.　The　rare　taxa　were　ubiquitous　in　all　soil　samples,　while　the　higher　Shannon　diversity　of　the　abundant　taxa　of　TK　may　be　related　to　the　habitat　preferences　of　species　and　niche　differentiation.　The　community　composition　of　bacterial　and　fungal　sub-communities　exhibited　significant　dissimilarity　between　TK　and　KL.　The　redundancy　analysis　further　demonstrated　that　abundant　taxa　were　environmentally　more　constrained　than　rare　taxa.　The　bacterial　and　fungal　networks　of　KL　were　more　complex　than　TK.　The　keystones　of　the　network　transforms　may　suggest　their　significant　role　in　the　ecological　function　of　the　karst　tiankeng　ecosystem.　This　study　represents　the　first　reports　of　the　characteristics　of　bacterial　and　fungal　communities　in　karst　tiankeng.　©　2022,　The　Author(s),　under　exclusive　licence　to　Springer-Verlag　GmbH　Germany,　part　of　Springer　Nature.