Summary Sequencing of 16S rDNA polymerase chain reaction ( PCR ) amplicons is the most common approach for investigating environmental prokaryotic diversity, despite the known biases introduced during PCR . Here we show that 16S rDNA fragments derived from Illumina‐sequenced environmental metagenomes ( mi tag s) are a powerful alternative to 16S rDNA amplicons for investigating the taxonomic diversity and structure of prokaryo...