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Fumonisins are important mycotoxins which often contaminate several cereals such as maize, wheat or rice, although they can also occur in a wide variety of other commodities. Fumonisins are responsible of serious chronic and acute diseases in human and animals and their presence is under regulation in more than 100 countries. Fumonisin production is basically limited to the members of the formerly so-called <i>Gibberella fujikuroi</i> species complex. <i>Fusarium fujikuroi</i> has been described as a maize and rice pathogen causing important agricultural losses. However, little information is available about the phylogenetics of this species and its ability to produce fumonisins in rice. In this work, we studied 23 strains isolated from rice in the Philippines and performed a phylogenetic analysis using the partial sequence of the elongation factor -1 alpha including isolates belonging to closely related species. Fumonisin production was analysed in seven-day-old cultures grown in fumonisin-inducing medium by an ELISA-based method and by real time RT- PCR using primers for <i>FUM1</i> gene, a key gene in fumonisin biosynthesis. The results indicated the ability of <i>F. fujikuroi</i> isolates to produce fumonisin at low levels in the conditions tested and a good agreement between results obtained by ELISA and real time RT-PCR. Fumonisin production of the isolates was not associated with their pathogenicity. High degree of variation was observed among the isolates using universally primed- polymerase chain reaction (UP-PCR) analysis, suggesting that sexual reproduction could play a significant role in generating variation of <i>F. fujikuroi</i> populations in the field.<p><p>Keywords: Fungus, Cereals-Grains, Rice