Staphylococcus aureusis a human commensal and opportunistic pathogen that can also colonise and cause disease in other animal species. In humans and livestock, whereS. aureusis most studied, there is evidence that strains have different host specialisms. Recent studies have foundS. aureusin many wild animals, including fish, whose physiologies and ecologies are very different to humans. However, it remains unclear whetherS. aureusis adapted to and persisting within these species, or if its presence is due to repeated spillover from a source population. Distinguishing between these two scenarios is important for both public health and conservation. In this study we looked for evidence to support the hypothesis that the presence ofS. aureusin fish is the result of spillover, through testing for the presence ofS. aureusin fish that are isolated from likely source populations. We sampled 123 brown trout and their environment from 16 sites in the Scottish Highlands. All these sites are remote and have very low populations density of wild animal species known to carryS. aureus, but were selected to represent variable levels of exposure to humans, avian and livestock species. While our sampling methods readily detectedS. aureusfrom the external and internal organs of a farmed fish, we did not detectS. aureusin any wild trout or their environment from any of the 16 sites. We sequenced 12S. aureusisolates from the farmed fish. While they were all from clonal-complex 45, the genomic diversity was high enough to indicate repeated acquisition from a source population. In addition, the presence of a φSa3 prophage containing a human immune evasion cluster indicates a recent history of these isolates within human populations. Taken together, our results support the presence ofS. aureusin fish being due to spillover from other host populations, rather than the adaptation of S. aureus to aquaculture or fish populations. Given predictions that fish consumption will increase, more whole genome sequencing ofS. aureusin aquaculture is needed to understand the presence ofS. aureusin these environments and to mitigate the risk to fish and human health.