The southern Prairie Pothole Region (PPR) of central North America is a highly modified landscape where remnant unplowed prairies could serve as repositories of native plant biodiversity. A previous study paired two historically idle US Fish and Wildlife Service (USFWS) National Wildlife Refuges with nearby privately owned grazing lands in North Dakota and found differences in invasive grass frequency, notably that smooth brome (Bromus inermis Leyss.) was less prevalent on annually grazed lands. A broader assessment, conducted over a wider geographic area, was warranted to investigate whether this relationship held across the southern extent of PPR in North Dakota and South Dakota. To this end, we selected 26 USFWS native prairie sites paired with adjacent/nearby native prairie sites with a history of livestock grazing in the PPR of North Dakota and South Dakota. We estimated plant species’ cover in five 10 × 10 m plots at each paired site in June or July of 2021. Plant community composition on USFWS sites was distinct from paired sites under private or state ownership (permutational analysis of variance (P = 0.021, F = 1.935). Additionally, paired t-tests revealed that sites under private or state ownership (with a long-term history of grazing) had higher total species richness (P = 0.006) and floristic quality index (a measure of species richness and disturbance tolerance) values (P = 0.042) than USFWS sites (without a long-term history of grazing). Smooth brome relative cover was lower (P = 0.019) at sites with a long-term history of grazing (13.4% mean relative cover) than paired USFWS sites (23.3% mean relative cover). Given these differences, remnant native prairies with long-term histories of annual grazing may provide unique opportunities for conserving native plant diversity and impeding smooth brome spread in the southern PPR.