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In September 2018, Hurricane Florence caused extreme flooding in eastern North Carolina, USA, a region highly dense in concentrated animal production, especially swine and poultry. In this study, floodwater samples ( n  = 96) were collected as promptly post-hurricane as possible and for up to approximately 30 days and selectively enriched for Campylobacter using Bolton broth enrichment and isolation on modified charcoal cefoperazone deoxycholate agar (mCCDA) microaerobically at 42°C. Only one sample yielded Campylobacter , which was found to be Campylobacter jejuni with the novel sequence type 2866 (ST-2866). However, the methods employed to isolate Campylobacter readily yielded Arcobacter from 73.5% of the floodwater samples. The Arcobacter isolates failed to grow on Mueller-Hinton agar at 25, 30, 37, or 42°C microaerobically or aerobically but could be readily subcultured on mCCDA at 42°C microaerobically. Multilocus sequence typing of 112 isolates indicated that all were Arcobacter butzleri The majority (85.7%) of the isolates exhibited novel sequence types (STs), with 66 novel STs identified. Several STs, including certain novel ones, were detected in diverse waterbody types (channel, isolated ephemeral pools, floodplain) and from multiple watersheds, suggesting the potential for regionally dominant strains. The genotypes were clearly partitioned into two major clades, one with high representation of human and ruminant isolates and another with an abundance of swine and poultry isolates. Surveillance of environmental waters and food animal production systems in this animal agriculture-dense region is needed to assess potential regional prevalence and temporal stability of the observed A. butzleri strains as well as their potential association with specific types of food animal production. IMPORTANCE Climate change and associated extreme weather events can have massive impacts on the prevalence of microbial pathogens in floodwaters. However, limited data are available on foodborne zoonotic pathogens such as Campylobacter or Arcobacter in hurricane-associated floodwaters in rural regions with intensive animal production. With a high density of intensive animal production as well as pronounced vulnerability to hurricanes, eastern North Carolina presents unique opportunities in this regard. Our findings revealed widespread incidence of the emerging zoonotic pathogen Arcobacter butzleri in floodwaters from Hurricane Florence. We encountered high and largely unexplored diversity while also noting the potential for regionally abundant and persistent clones. We noted pronounced partitioning of the floodwater genotypes into two source-associated clades. The data will contribute to elucidating the poorly understood ecology of this emerging pathogen and highlight the importance of surveillance of floodwaters associated with hurricanes and other extreme weather events for Arcobacter and other zoonotic pathogens., (Copyright © 2020 Niedermeyer et al.)