The replacement of natural areas by urban areas promotes changes in the composition of tree communities, frequently favoring the occurrence of exotic species. This may have direct implications in the structure of pathogenic fungal communities which grow in these hosts. Here we examine: a) the structure of the interaction networks between urban tree species and their pathogenic wood-decay fungi, b) the composition of pathogenic fungi in native and exotic hosts. The interactions network shows a nested pattern where several species of pathogenic fungi establish multiple interactions with various tree species, both native and exotic; while others establish more specific interactions. Richness of pathogenic fungi was higher in exotic trees than in natives. Thirteen fungal species occurred exclusively in exotic hosts, one in natives and the remaining nine species shared both exotic and native hosts.