Significance The neurotoxin-producing dinoflagellate Alexandrium catenella is shown to be distributed widely and at high concentrations in bottom sediments and surface waters of the Alaskan Arctic. Future blooms are likely to be large and frequent given hydrographic and bathymetric features that support high cell and cyst accumulations, and warming temperatures that promote bloom initiation from cysts in bottom sediments and cell division in surface waters. As the region undergoes an unprecedented regime shift, the exceptionally widespread and dense cyst and cell distributions represent a significant threat to Arctic communities that are heavily dependent upon subsistence harvesting of marine resources. These observations also highlight how warming can facilitate range expansions of harmful algal bloom species into waters where temperatures were formerly unfavorable.