The emergence of bacterial infections caused by resistant strains poses a threat to the development of new antibiotics. The majority of antibiotics being produced has been accelerated through the finding of newly reported natural products, especially those originated and produced by biological sources. Endophytic fungi residing in medicinal plants may be regarded as potential sources and encourage the exploration of more plant species for their antimicrobial activity. Our current study reports on the assemblage of endophytic fungi that colonize the rhizomes, using Globba patens a representative of Zingiberaceous species from North Sumatra. Twenty-six fungal morphotypes were obtained and differentiated by their morphological features. Each isolate was tested against human pathogenic bacteria namely Staphylococcus aureus ATCC® 29213™, Methicillin-resistant S. aureus (MRSA) ATCC® 43300™, Escherichia coli ATCC® 25922™, and Enteropathogenic E. coli (EPEC) K11 in a dual culture assay. The results revealed that the majority of fungal isolates were strong antagonists against S. aureus and E. coli but not against MRSA and EPEC. Isolate Gp07 was the most potential fungus with a wide range of antibacterial activities and was subjected to further species-level identification based on its morphological characteristics and DNA sequence in the ITS-rDNA region. The isolate Gp07 was identified as Colletotrichum siamense, yet the presence of C. siamense in the rhizome of G. patens is not fully understood while possibly being characterized as the antibiotics-producing agent in the future.