This project contains the near full-length 16S rRNA gene data belonging to the Microflora Danica project. The Microflora Danica project encompasses over 10,000 samples from across Denmark, taken between 2019 and 2023 with the goal to cover as much of the microbial diversity in the investigated habitats as possible. For the bacterial 16S UMI rRNA gene data and eukaryotic operon data see https://doi.org/10.15468/33qqsm and https://doi.org/10.15468/ea7jvq, respectively. In the project the UMI 16S rRNA gene sequences was used together with near full-length 16S rRNA gene sequences to construct the Microflora Danica 16S rRNA gene reference database (https://zenodo.org/records/12605769) and to investigate the 16S rRNA gene sequence diversity and novelty of species representative sequences. Furthermore, the UMI 16S rRNA gene data was solely used for the estimation of the bacterial richness of the Danish terrestrial habitats and in the analysis of different diversity metrics in the manuscript (https://doi.org/10.1101/2024.06.27.600767). DISCLAIMER: The 16S rRNA gene data from the bacterial operons should be used for investigation of occurrence only, and are not fit for analysis of diversity metrics: Funding was provided by the Poul Due Jensen/Grundfos Foundation. Associated metadata is also available from github (https://github.com/cmc-aau/mfd_wiki).[This dataset was processed using the GBIF Metabarcoding Data Toolkit.]