Staphylococcus aureus is an opportunistic human pathogen that can cause pneumonia, endocarditis, osteomyelitis, and skin infections, leading to septicaemia and death. Multi-drug resistant S. aureus (MRSA) infections are still rare, but an alarming number do not respond to antibiotic treatment due to intermediate antibiotic tolerance. MRSA with reduced vancomycin-susceptibility (vancomycin intermediate S. aureus, VISA) accumulate chromosomal mutations that lead to changes in cell physiology like cell wall thickening, reduced autolysis, and altered acetate metabolism. Transcriptional profiling of vancomycin susceptible MRSA after treatment with sub-inhibitory concentrations of last line antibiotics demonstrated that regulatory small RNAs form a coherent response to antibiotic challenge across a number of MRSA isolates. We have recently developed a UV-crosslinking technique in E. coli, termed RNase-CLASH, that allows transcriptome-wide profiling of sRNA-mRNA interactions in vivo. RNase E-CLASH is dependent on sRNA-mRNA interactions with the RNA degradosome scaffold protein, RNase E, but this protein is not present in Staphylococcus. In an effort to understand how sRNAs adapt MRSA to antibiotic stress, we have developed CLASH for MRSA. To find a suitable ‘scaffold’ to capture sRNA-mRNA interactions, we have epitope-tagged the Staphylococcal RNA degradosome components RNase J1, RNase J2, RNase Y, and RNase III and performed UV-crosslinking. We recovered 636 sRNA-target RNA interactions in complex with RNase Y and RNase III, demonstrating the feasibility of our approach. We found multiple interactions between sRNAs and transcripts implicated in antibiotic resistance and the VISA phenotype. We confirmed these interactions using GFP translational fusions and selected interactions will be discussed. This study presents the first transcriptome-wide, in vivo profiling of the sRNA regulatory landscape in Staphylococcus aureus and provides valuable insights into how sRNA regulation adapts the cell to acute antibiotic stress and contributes to antibiotic tolerance.