SRP189042 PRJNA528395 Raw genome sequence data for 13 isogenic Aspergillus fumigatus strains isolated from one patient. Here we present the whole genome sequences of 13 clinical isogenic Aspergillus fumigatus isolates. These isolates were cultured from a single patient suffering from invasive aspergillosis over a period of 2 years. This patient underwent a wide range of antifungal therapies and the resultant isolates acquired multiple azole resistance in-host during the course of infection.