Endophytic and epiphytic fungal assemblages from stems of S. rotundifolia a shrubby vine were studied in order to (1) quantify differences and the degree of overlap between fungal communities of both micro-habitats and (2) examine whether fungal assemblages are spatially correlated at the local scale (tens to hundreds of meters) in order to understand if dispersal limitation may play a role in structuring these communities. Sampling was conducted over 160 m of growth along a forest edge. The communities showed low overlap (Bray-Curtis Similarity?=?0.22) with most species that were common in one habitat appearing rarely if at all in the other and only Aureobasidium pullulans showing high frequency in both. Epiphytic assemblages proved to be spatially correlated along the 160 m length of the transect and even more so when adjacent pairs of stems were considered as the unit of comparison rather than individual stems. Endophytic assemblages showed no significant spatial correlation along the transect. Unexpectedly three species of endophytes showed a pattern in which abundance of colonies peaked at different heights on the stems. Colletotrichum boninense showed peak abundance at 3 cm from the stem base. Phomopsis sp. 1 peaked at 33 cm from the stem base. Endophytic isolates of A. pullulans peaked at 63 cm from the stem tip. It was also found that positive correlative relationships were detected between endophyte-endophyte and epiphyte-epiphyte pairs. Cross-group interactions seemed to center around crossover species that were not entirely constrained within the surface or interior.