R.R. Yurong, P.J. Geraldino, Molecular Characterization, Phylogeny and Flavonoid Secretions of Fungal Endophytes Isolated from Species of Tree Fern, Cyathea contaminans (Hook) Copel from the Philippines, Botany Research Journal, Volume 12,Issue 3, 2019, Pages 37-41, ISSN 1995-4751, brj.2019.37.41, (https://makhillpublications.co/view-article.php?doi=brj.2019.37.41) Abstract: This study was conducted to identify and describe the phylogenetic positions of the species of fungal endophytes isolated from Cyathea contaminans (Hook) Copel using the molecular character, the ITS1-5.8sRNA-ITS2 gene sequence. A total of nine species were identified by comparing the isolates gene sequence with the sequences from the genbank.The phylogeny of the species was also described using the Maximum Parsimony Tree (MP). Moreover, the fungal extracts were also subjected to Shinoda’s Test and UV-Vis spectrophotometry to determine their flavonoid secretions. The species identified include the: Aspergillus sydowii, Colletotrichum gloeosporioides, Fusarium kyushuense, Fusarium pseudensiforme, Fusarium solani, Nigrospora sphaerica, Nectria hematococca, Penicillium citrinum and Penicillium griseofulvum. The MP tree revealed the clustering of three species belonging to Fusarium solani species complex (N. hematococca, F. pseudensiforme and F. solani) and with Fusarium kyushuense they are held under order Hypocreales Another group the A.sydowii, P. citrinum and P. griseofulvum represented the order Eurotiales. N. sphaerica under order Trichosphaeriales was positioned basal to the Hypocreales and C. gloeosporiodes under Phyllachoralles was basal to Eurotiales. Phytochemical analysis revealed that all the endophytic fungal isolates except A. sydowii produced flavonoids. There were five flavonoid types secreted by the isolates namely: Band B flavones and flavonols, Band A flavones, Band A flavonols, Band A flavanones and Band B flavanones. All isolates produced the flavonoids with N. sphaerica positive to all the five types and A. sydowii negative to all. Here, the endophytic fungal isolates from C. contaminans can be identified to species level by the ITS1-srRNA-ITS2 gene sequence and are good prospects for bioprospecting. Keywords: Endophytes;eurotiales;flavonoids;hypocreales;cyathea