Fusarium head blight (FHB) has become a limiting factor to soft red winter wheat production in Georgia and Alabama in recent years partly due to an increase in acreage of corn, another host for some FHB fungi. FHB is caused by 16 biogeographically diverse species within the Fusarium graminearum species complex (FGSC) although F. graminearum sensu stricto (s.s.) with its 15ADON (type B trichothecene) chemotype is predominant in the US and Canada. To investigate the genetic diversity of this pathogen in GA and AL, we collected nearly 150 isolates from symptomatic wheat heads and corn debris from 23 counties of the two states in 2018. PCR-based identification with translocation elongation factor 1 alpha (EF-1?) primers indicated most isolates were F. graminearum s.s. with a few of the recovered isolates being F. poae. Chemotyping using multiplex PCR targeting the Tri3 and Tri12 genes revealed the isolates so far are 15ADON type. Phylogenetic analysis of representative isolates and reference strains of all known FGSC species based on the EF-1? gene showed that most of the isolates were clustered within the F. graminearum clade. To our best knowledge, this is the first investigation of FGSC along with chemotype identification in the region. However, additional sampling and further studies on the population structure, chemotype, and virulence of the isolates are needed to better understand the pathogen to assist in developing adequate disease management strategies.