Antimicrobial resistance genes are often encoded on mobile genetic elements that are transferrable between pathogens. Transfer of AMR genes between methicillin-resistant Staphylococcus aureus (MRSA) occurs at high frequency during colonization of the host, due to generalized transduction by endogenous prophage. In this study we investigated the role of sub-inhibitory antibiotics on the induction of transfer. Nine different antibiotics induced transfer of an erythromycin resistant plasmid between clinical MRSA isolates. Unexpectedly, transduction frequency was not correlated with the induction of free endogenous phage, so that each antibiotic generated a unique ratio of transducing and infectious phage particles. UV stress dramatically increased transduction induced by trimethoprim and cefoxatin (a b-lactam), and this was correlated with induction of infectious phage. Novobiocin and gentamicin reduced the UV stress induced transduction and phage release, but had less effect on antibiotic induced transfer. Using new technology, digital droplet PCR, we could accurately quantitate DNA in phage particles, suggesting that antibiotics and UV both act by altering packaging of DNA into phage heads. In summary, the mechanisms of antibiotic induction and suppression of generalized transduction are different to UV stress induction, and during colonization of the host, antibiotic exposure affects transfer and evolution of resistances in MRSA populations.