Selective spore trapping and molecular genotyping methods were employed to examine potential long-distance gene flow among Caribbean populations of the common mushroom Schizophyllum commune. Spore-trap samples from five locations were analysed using restriction fragment polymorphisms of five enzymatically amplified gene regions. Successful trappings suggested S. commune spores to be abundant in the air, with an estimated sedimentation rate of approximately 18 spores/m2/h. High levels of genetic diversity characterized the spore-trap samples, with as many as 12 alleles observed at a single locus (chitin synthase) over all samples. In addition, spore-trap samples showed significant among sample heterogeneity including geographical population substructure. The ribosomal DNA (rDNA) intergenic spacer displayed the greatest allele frequency differences among samples, clearly separating the samples into those possessing only a South American-type allele and those segregating for both North and South American-type alleles. The molecular variation provided no clear evidence for dispersal over large, aquatic barriers within the Caribbean region, and instead suggested that spore-trapping experiments are primarily reflective of the local, established population.