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<p>Abstract</p> <p>Background</p> <p><it>Aspergillus terreus </it>causes invasive aspergillosis (IA) in immunocompromised individuals and can be the leading cause of IA in certain medical centers. We examined a large isolate collection (n = 117) for the presence of cryptic <it>A. terreus </it>species and employed a genome scanning method, Inter-Simple Sequence Repeat (ISSR) PCR to determine <it>A. terreus </it>population structure.</p> <p>Results</p> <p>Comparative sequence analyses of the calmodulin locus revealed the presence of the recently recognized species <it>A. alabamensis </it>(n = 4) in this collection. Maximum parsimony, Neighbor joining, and Bayesian clustering of the ISSR data from the 113 sequence-confirmed <it>A. terreus </it>isolates demonstrated that one clade was composed exclusively of isolates from Europe and another clade was enriched for isolates from the US.</p> <p>Conclusions</p> <p>This study provides evidence of a population structure linked to geographical origin in <it>A. terreus</it>.</p>