Prolonged respiratory infection by the opportunistic pathogen, Pseudomonas aeruginosa, is the major contributor to early mortality in individuals with cystic fibrosis (CF). Patients often acquire their infections from the environment, however it is unknown whether all genotypes are capable of causing infection. To investigate this, we experimentally evolved 18 environmental and CF-clinical genotypes within synthetic CF lung sputum (SCFM), to identify any genotypic and/or prior niche constraints on trait evolution and pathoadaptation. We found that genotype significantly constrained evolution within SCFM, which was evidenced through phylogenetic signal in the change of both traits and fitness. We also found that environmental strains evolve differently in SCFM compared to their CF-clinical counterparts. Altogether our results suggest there is widespread variation in the adaptation of P. aeruginosa, which is in part constrained by both genetic background, and niche of origin.