In 2020, an evaluation of the basal level of incidence of tomato spotted wilt (TSW) in peanut was initiated in Alabama. This was done to understand the viral sequence divergence of tomato spotted wilt virus (TSWV) in a heavily managed system. From 2021 to 2023, 172 leaf samples were collected from peanut plants exhibiting symptoms of TSW from Brewton, Fairhope, and Headland, AL, to investigate genetic changes. Additionally, four thrips populations were collected in 2022 and 2023 from Fairhope and Headland, AL. The nucleocapsid protein of TSWV was sequenced from both leaf samples and thrips. A total of 175 nucleocapsids were sequenced, and their amino acid sequences were aligned to identify three conserved mutations compared to TSWV-MT2 (X61799.1) and seven conserved mutations when aligned against TSWV-BR-01 (NC_002051.1). Interestingly, only one conserved mutation was found in the thrips sequences compared to MT2, and no mutations were detected when aligned with BR-01. To identify if mutations caused a phenotype that could be measured, eight nucleocapsids with unique mutations were selected for localization in Nicotiana benthamiana. The localization patterns of these proteins were grouped into three phenotypes based on the observed protein aggregation speed. Small-plot trials assessed TSWV mutations and incidence in relation to planting date, insecticide use, and cultivar. Based on these data, although management strategies are effective at keeping levels of TSWV manageable, the virus can diversify its sequence, which causes changes in the expected phenotype of the nucleocapsid.