Bacterial sRNAs are small and highly structured RNA molecules whose complex role in regulating prokaryotic gene and protein expression has only recently been realised. Several sRNA families have been found to regulate virulence factors in pathogenic bacteria, and many are expressed in response to specific environmental pressures, making them a pressing area of study. Despite their important biological function, the annotation and discovery of sRNAs is hindered by a lack of sequence conservation across the tree of life. We are investigating the use of hidden markov models (HMMs) to improve sRNA search methods and better understand the mechanisms behind their origins and rapid evolution.