The universal presence and consistent size of the 16S ribosomal RNA gene have defined it as the hallmark phylogenetic marker for classifying bacteria and archaea. Salman et al. now challenge this view by revealing that large sulphur bacteria contain a number of self-splicing introns at specific sites in this gene that can increase its size by up to 3.5 kb. The four introns had low sequence identity, and phylogenetic analysis of the most recurrent intron showed that it was probably transferred both vertically and horizontally within this bacterial family. These introns were capable of self-splicing in vitro and were removed from precursor 16S rRNA, indicating that they do not disturb ribosome function. The discovery of introns in the most commonly sequenced gene is a surprise and also questions the reliability of this phylogenetic marker for diversity studies because heterogeneity in the size of the 16S rRNA gene is not taken into consideration by many common detection techniques.