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<div><i>To avoid publishing twice, the original abstract will be published with the other “<b>Southern Division 2017</b>” abstracts in Phytopathology.</i><p>Stem rot is one of the most important soilborne diseases in the Southeastern US, causing significant yield loss in tomato, pepper, and peanut. Population structure and genetic variation of the causal agent, <i>Sclerotium rolfsii</i>, is yet to be explored for Southeastern isolates, despite significant variability in colony morphology and host virulence. Mycelial compatibility groups have indicated the possibility of genetic diversity and previous phylogenetic analysis of the non-coding internal transcribed spacer (ITS) region indicate sequence variation among Florida isolates. The objective of this study was to determine the number of genotypes in the Southeastern US using sequence analysis of a protein coding gene. Thirty-five isolates infecting peanut in Florida, Georgia, and Alabama were collected and whole genomic DNA was extracted. RNA polymerase II subunit I (Rpb1) protein was amplified and sequenced. Sequences were analyzed using the Templeton, Crandall, Sing (TCS) algorithm for determining phylogenetic networks, where each node in the network is a genotype and links between nodes represent mutational steps. This study reports the first phylogenetic network for <i>S. rolfsii</i> in the Southeastern US using a protein coding gene sequence. Genotypes in the Southeastern US were distinct from previously characterized Mediterranean genotypes. Knowledge of gene flow among populations of <i>S. rolfsii</i> is needed for durable host resistance and can improve disease management.</div>