Fusarium head blight (FHB) caused by Fusarium graminearum (Fg), an ascomycete fungi, is a persistent disease of cereal crops in world food baskets including South Dakota, and a serious threat to the quality and quantity of grain production in wheat, barley, triticale, and oats. Fusarium secretes various mycotoxins that are harmful to humans and animals making infected grain unsuitable for food and feed. Being a broad host range pathogen, its genome related to virulence, mycotoxin production, and yet to be characterized plant-pathogen-interaction loci are continuously incorporating nucleotide changes responding to host immunity. These changes and their maintenance in the genome correspond to their potential utility in pathogen survival fitness, and phenotypes related to host adaptations resulting in fluidic spatio-temporal pathogen genome diversity. Thus, our goal is to study temporal pathogen genome diversity in relation to the diverse small grain hosts. To do so, we sequenced 23 Fg isolates collected from barley, wheat, and oat fields in South Dakota from 2012 to 2022 using the Illumina Nextseq500 platform. For genome analysis, we used both denovo assembly as well as reference-based reads mapping to both genome and the mycotoxin-producing Tri gene cluster. In our approach, we used 5 different assembly tools (for short and paired-end reads) and found SPAdes works best for our data. Ongoing work includes whole genome comparison and diversity analysis focusing on mycotoxins related well-studied genes Tri5 and Tri3. We aim to characterize putative genetic shift in the pathogen genome accounting for the additional layer of complexity of its evolution on multiple hosts affecting strategies of resistance deployment.