A total of 36 fungal endophytes were isolated from apparently healthy sweet potato plants from leaves, stems and roots collected from Baguio City. Among the isolates, only P3AL2c (GenBank accession no. JN672600.1) and P3BS1c (GenBank accession no. JN672605) significantly enhanced growth of paclobutrazol treated rice seedlings. The genomic DNA of these two fungal endophytes were isolated and ran on PCR using ITS 1 and ITS 4 primers. The PCR products were sequenced and subjected to BLASTn for detection of homology to Genbank accessions. P3AL2c was closest to Fusarium oxysporum isolate UOA/HCPF and P3BS1c was most homologous with Emericella nidulans strain FH5. Phylogenetic analysis using maximum likelihood algorithm with 1000 bootstrap replications generated the phylogenetic affinities of the isolates with Fusarium/Gibberella clade and Emericella nidulans, respectively.