Floriculture is one of the fastest growing agribusiness segments in Brazil, especially the tropical flowers market, which is favored by the climatic conditions of the different regions of the country, especially the northeast region. Within this sector, the production of orchids represents a type of trade in increasing expansion in the national market and this is due to the diversity, beauty of its flowers and its easy cultivation. However, despite the progress, orchid culture has been limited by several factors, among which are the occurrence of diseases, especially those of fungal origin. Knowing the etiologic agent is essential for the success, durability and large-scale implementation of control measures. Therefore, the objective of the present work was to identify fungal species associated with native or commercial orchids based on the analysis of morphocultural and phylogenetic characteristics. They were identified based on isolated morphological characters belonging to the genera Colletotrichum and Fusarium. According to the BLAST search of the GenBank database and the analysis of partial sequences of the glyceraldehyde-3-phosphate dehydrogenase (GAPDH) gene, the isolates of the genus Colletotrichum were grouped into the complexes of C. gloeosporioides, C. orchidearum, C. gigasporum and C. dracaenophilum. The Fusarium isolates are distributed in the complexes of F. incarnatum –equiseti, F. fujikuroi and F. oxysporum, based on the phylogenetic analysis of the partial sequences of the translational elongation factor 1-α (TEF-1α) and second largest gene. RNA polymerase II subunit (RPB2).