Frogeye leaf spot (FLS), caused by Cercospora sojina, causes significant damage to soybean in the U.S. One control strategy is the use of quinone outside inhibitor (QoI) fungicides. QoI resistant isolates were first reported in Tennessee (TN) in 2010. To investigate the disease dynamics of C. sojina, we collected 437 C. sojina isolates in 2015 from Jackson and Milan, TN and used 40 historical isolates collected from 2006-2009 from TN and ten additional states for comparison. A subset of 186 isolates, including historical isolates, were genotyped for 49 single nucleotide polymorphism (SNP) markers and the QoI resistance locus, revealing 35 unique genotypes. The genotypes clustered into three groups with two groups containing only sensitive isolates and the remaining group containing all resistant isolates and a dominant clonal lineage of 130 isolates. All 477 C. sojina isolates were genotyped for the QoI locus revealing 344 resistant and 133 sensitive isolates. All isolates collected prior to 2015 were QoI sensitive. Both mating type alleles (MAT1-1-1 and MAT1-2) were found in Jackson and Milan, TN and recovered from single lesions suggesting sexual recombination may play a role in the epidemiology of field populations. Analysis of C. sojina isolates using SNP markers proved useful to investigate population diversity and to elaborate on diversity as it relates to QoI resistance and mating type.