Discovered in the 1980s, small regulatory RNAs (sRNAs) are now considered key actors in virtually all aspects ofbacterial physiology and virulence. Together with transcriptional and translational regulatory proteins, theyintegrate and often are hubs of complex regulatory networks, responsible for bacterial response/adaptation tovarious perceived stimuli. The recent development of powerful RNA sequencing technologies has facilitated theidentification and characterization of sRNAs (length, structure and expression conditions) and their RNA targetsin several bacteria. Nevertheless, it could be very difficult for non-experts to understand the advantages anddrawbacks related to each offered option and, consequently, to make an informed choice. Therefore, the maingoal of this review is to provide a guide to navigate through the twists and turns of high-throughput RNAsequencing technologies, with a specific focus on those applied to the study of sRNAs.This article is part of a Special Issue entitled: RNA and gene control in bacteria edited by Dr. M. Guillier and F.Repoila.