Riboswitches are vital components of many genomes. Covariance model searches for the characteristic architectures of riboswitch aptamer domains can be used to predict new examples of these structured RNAs. Since riboswitches generally function as cis-regulatory elements, examining the genomic contexts of these hits is critical for evaluating their biological relevance. With these two sources of comparative support, it is possible to identify riboswitches accurately from sequence information alone. Annotating riboswitches on a genomic scale enables more precise functions to be assigned to the proteins that they regulate, better defines their conserved aptamer structures by identifying diverged variants, and provides insight into how the genetic regulation of fundamental metabolic processes varies among species.