Several species belonging to the Gibberella fujikuroi species (Gf) complex are commonly associated with rice and corn, not only causing serious diseases, but also producing fumonisins, a group of mycotoxins harmful to animals and humans. To characterize the population structure of the putative fumonisin-producing Gf complex in Korea, we obtained 276 candidate isolates from rice and corn harvested in 2009 and 2010 by diagnostic polymerase chain reaction with several specific primer sets. Phylogenetic trees were constructed using multilocus sequences (combined RPB2 and EF1A, totaling 1.6 kb) from these isolates. Among the 135 isolates from rice, F. fujikuroi (teleomorph: G. fujikuroi; 59.3%) and F. proliferatum (G. intermedia; 13.3%) were predominant, followed by F. concentricum (5.9%). Additionally, twentyfive (18.5%) rice isolates belonged in a distinct subclade of F. commune, a non-member of the Gf complex. In contrast, F. verticillioides was the most predominant species (38.3%) among the 141 corn isolates, and followed by F. fujikuroi (27.7%), F. proliferatum (14.9%), F. subglutinans (7.1%), and F. concentricum (2.8%). A single mating type (MAT1-1) was found predominantly among the Gf complex isolates examined. Possible distinct subclades were detected within the populations of F. fujikuroi and F. proliferatum; however, this needs further confirmation. This is the first reported population-level characterization of putative fumonisin-producing Gf complex associated with rice and corn in Korea.