Detrimental and beneficial interactions between bacteria represent the key to the understanding of the processes that allow the development and persistence of respiratory infections. In cystic fibrosis (CF) patients, the lung microbiota is altered in favor of pathogenic bacterial species such as Staphylococcus aureus, the most prevalent colonizing bacteria in young patients, whereas up to 75% of adults are colonized by Pseudomonas aeruginosa. This work explored the adaptive strategy of P. aeruginosa to a pre-established S. aureus population, and the transcriptional responses triggered by the encounter of these two respiratory pathogens. This study shows that P. aeruginosa adapts to the presence of S. aureus by acquiring mutations in the lipopolysaccharide biosynthesis pathways. Furthermore, transcriptional profiling showed that the encounter caused a significant stress on each bacterium.