Endophytic fungi were identified from different parts of the medicinal parasitic mistletoe Cladocolea micrantha and from its host Anacardium occidentale, suggesting a strict host-parasite relationship. Eight fungal endophytes were isolated and morphologically characterized. The ascomycete Guignardia mangiferae and strains of Mycelia sterilia were prevalent in the isolations. The unequivocal identification of Guignardia mangiferae at a probabilistic degree close to 100% was carried out by DNA extraction followed by PCR analyses of the ITS-1 and ITS-2 regions and comparison of the genetic sequence with the NCBI database.