Banana plants, scientifically known as Musa acuminata Colla, are a vital crop for the Philippines, a major exporter of bananas worldwide. Concerns have emerged regarding the presence of pathogenic Fusarium species in key banana production regions. To address this, a study was conducted to identify and characterize the fungal community associated with banana pseudostems in Regions X, XI, and XII. Genomic DNA was extracted from isolated cottony fungi, and the internal transcribed spacer (ITS) region was amplified using polymerase chain reaction (PCR). A total of 20 fungal isolates were identified, comprising nine Fusarium species, 10 Trichoderma species, and one Pleurotus species. Among the identified species, F. oxysporum was the most abundant and showed high genetic variation, suggesting successful adaptation to local conditions. Phylogenetic analyses revealed close relationships among F. oxysporum isolates from South Cotabato and General Santos City, with potential transmission to Davao del Sur. Similarly, T. virens isolates from South Cotabato showed close relationships with those from Bukidnon and Davao del Sur. The presence of Trichoderma species, including newly discovered presence of T. pleuroticola, T. amazonicum, and T. afroharzianum in banana pseudostems, as well as the isolation of P. ostreatus, indicates their potential as biocontrol agents against Fusarium species. The study recommends the need for improved quality of sequences, increased sample sizes, and the implementation of biological control measures to effectively manage the fungal community associated with banana pseudostems and mitigate the risks posed by Fusarium infections.