Dahlia variabilis has many beneficial effects to human health, such as antibacterial and antifungi agent. This research aimed to discover the potency of endophytic microbesisolated from Dahlia as antimicrobial agents. Screenings were carried out using agar diffusion method against pathogens with concentration of 50μl/disc. Based on our previous study, four isolates of endophytic fungi were isolated and characterized morphologically as follows, LBKURCC40 identified as Monilia sp., LBKURCC41 identified as Aureobasidium sp., LBKURCC42 identified as Moniliella sp., and LBKURCC42 identified as Sporothrix sp. The inhibition zone of amoxsan was 12.55 ±0.38 mm and ketoconazole was 17.67±0.57 mm. LBKURCC41 showed the most significant inhibition zones against Eschericia coli and Staphylococcus aureus which those were 19.33±1.15 mm and 17.00±1.00 mm respectively. LBKURCC41 was then characterized genetically. The molecular weight of chromosomal DNA of LBKURCC41 obtained was 11,706 bp. Its rDNA was amplified with PCR using ITS5 and ITS4 as DNA primers and the result of phylogenetic analysis at ITS-1, ITS-2 and 5.8S rDNA showed that LBKURCC41 was Fusarium oxysporum with 99% similarity, which was different from previous morphological characterization.