Phialocephala fortinii is a common root endophytic fungus with a wide geographic distribution and little, if any, host specificity. Little is known about its habitat specificity, although there is evidence to suggest that high water tables may restrict the occurrence of P. fortinii in wetlands. We tested this hypothesis by determining the distribution of P. fortinii along a sand dune – wetland complex. Isolates of P. fortinii, identified on the basis of cultural and morphological characteristics, were obtained from the roots of vascular plants across the moisture gradient. Three ‘cultural groups’ were recognized among these isolates. Thirty-three of these isolates were compared among themselves and to strains of known identity using PCR/RFLP analysis of the ITS region and a portion of the 28S subunit of rDNA. The restriction digest profiles of all isolates were identical to those of P. fortinii for 4 restriction enzymes. DNA sequences, from a subset of these strains, showed a low percent sequence divergence confirming the reliability of the RFLP data. The same analyses were done with two strains of Leptodontidium orchidicola, a culturally similar root endophyte, to ensure that this taxon was not among the transect isolates. DNA data showed a clear difference between P. fortinii and L. orchidicola but did not discriminate among cultural groups. Thus, P. fortinii showed no habitat specificity and occurred in both xeric and hydric sites. RFLP profiles and ITS sequences showed little variation among isolates of P. fortinii and among the isolates of L. orchidicola.