A survey of endophytic Pestalotiopsis associated with two orchid species collected in Coco Island in Costa Rica was carried out. Among the fungi isolated from leaves of the two species, genus Pestalotiopsis prevailed. We isolated 29 strains of Pestalotiopsis, 9 of which from Camaridium micranthum M. A. Blanco and 20 from Ornithidium adendrobium (Rchb.f.) M.A. Blanco. On the basis of morphological characters, Pestalotiopsis isolates were divided into three different groups but their high similarity do not allow unambiguous species identification. The analysis of internal transcribed spacer (ITS) region of ribosomal DNA was then performed to evaluate the taxonomic position of our isolates.