Genetic diversity and identification of fumonisin-producing isolates of Fusarium verticillioides from two provinces in the Philippines were analyzed using molecular techniques. Using a Polymerase Chain Reaction (PCR)-based technique, 49 of the 54 isolates were identified as F. verticillioides, with an amplified product of 800 bp using VERT-1 and VERT-2 primers. Of these, VERTF-1/VERTF-2 primers detected 38 fumonisin-producing F. verticillioides isolates producing a single fragment of 400 bp. The other five isolates, which had previously been identified as F. verticillioides by TEF sequences, morphology and sexual crosses, were negative using this method. Using Universally Primed-PCR (UP-PCR) markers for F. verticillioides, no grouping was observed based on geographical origin and species, but intermediate (53.8%) to high (99.6%) bootstrap values and high genotypic diversity (H=0.99) were generated, suggesting that all isolates clearly belonged to F. verticilliodes. Unweighted Pair Group Method with Arithmetic Mean (UPGMA) cluster analysis with Jaccard's coefficient showed that similarities among F. verticillioides isolates were intermediate at 71% similarity level.