Most fungal species from marine environments also live on land. It is not clear whether these fungi reach the sea from terrestrial sources as spores or other propagules, or if there are separate ecotypes that live and reproduce in the sea. The emergence of marine diseases has created an urgency to understand the distribution of these fungi. Aspergillus flavus is ubiquitous in both terrestrial and marine environments. This species is an opportunistic pathogen in many hosts, making it a good model to study the relationship between genetic diversity and specificity of marine fungi. In this study, an intraspecific phylogeny of A. flavus isolates based on Amplified Fragment Length Polymorphisms (AFLPs) was used to determine if terrestrial and marine isolates form discrete populations, and to determine if phylogeny predicts substratum specificity. Results suggest lack of population structure in A. flavus. All isolates may compose a single population, with no clade particular to marine environments.