The first evidence of sexual reproduction inAspergillus fumigatuswas reported in 2009. Nevertheless, it remains difficult to understand howA. fumigatusis able to reproduce through this mode in its natural environment and how frequently this occurs. The aim of this study was to analyse single nucleotide polymorphisms (SNPs) in a set of environmental and clinical isolates ofA. fumigatusto detect signatures of recombination. A group of closely related PortugueseA. fumigatusisolates was characterized by mating type and the genetic diversity of the intergenic regions, microsatellites and multilocus sequence typing (MLST) genes. A group of 19 SNPs, organized in nine association groups and inherited in blocks, was identified and compared. Several variations on the association panel were detected on reference isolates ofA. fumigatusAF293 and A1163, the sequence types available at MLST database and six clinical and environmental Portuguese isolates. About one to four haplotype disruptions were observed per isolate. Considering clinical and environmental isolates, sexual reproduction seems to occur more frequently than previously admitted inA. fumigatus. In this study, a practical SNP approach is proposed for detection of recombination events in larger collections ofA. fumigatus.