Next-generation sequencing technologies have impressively unlocked capacities to depict the complexity of microbial communities. Microbial community structure is for now routinely monitored by sequencing of 16S rRNA gene, a phylogenetic marker almost conserved among bacteria and archaea. Nevertheless, amplicon sequencing, the most popular used approach, suffers from several biases impacting the picture of microbial communities. Here, we describe an innovative method based on gene capture by hybridization for the targeted enrichment of 16S rDNA biomarker from metagenomic samples. Coupled to near full-length 16S rDNA reconstruction, this approach enables an exhaustive and accurate description of microbial communities by enhancing taxonomic and phylogenetic resolutions. Furthermore, access of captured 16S flanking regions opens link between structure and function in microbial communities.