Aspergillus fumigatus is associated with various invasive, chronic, and allergic fungal diseases. The emergence of environmental azole-resistant strains complicates the treatment of these infections. The use of whole-genome sequencing (WGS), which is widely used to study bacterial and viral outbreaks, could be beneficial for characterizing azole-resistant A. fumigatus outbreaks. Here, nine azole-resistant cyp51A TR34/L98H A. fumigatus strains isolated during an outbreak in a French hospital between November 2021 and October 2022 were studied. The genetic relatedness of these strains was assessed using microsatellites, high-quality single-nucleotide polymorphisms (SNPs) from WGS data, phylogenetic reconstruction, and principal component analysis. Multiple sequenced but independently cultured A. fumigatus strains were used as identical strain controls. Among the nine unrelated patients infected by TR34/L98H A. fumigatus, five had previously isolated A. fumigatus strains without the cyp51A TR34/L98H mutation. Both microsatellites and WGS confirmed that the initial cyp51A wild-type strains for these five patients were genetically different from the new mutant strains. Eight of the nine TR34/L98H strains were genetically close, with a number of SNPs similar to the controls. These resistant strains were not related to four environmental strains isolated in the hospital. Altogether, the results suggest that at least eight patients were exposed to a common source, although its exact origin could not be determined. The presence of antifungal-resistant strains in healthcare settings underscores the need for active research into resistant strains and that both microsatellites and WGS techniques have their place in the management of A. fumigatus epidemics.