Clary sage (Salvia sclarea L.) is a winter specialty crop grown in northeastern North Carolina for the production of sclareolide, which is a fixative used in the fragrance industry. Poor stand establishment, plant stunting, and reduced yields are common problems that are exacerbated under wet conditions. In October 2018, 15 isolates of Pythium spp. were recovered from the roots of severely stunted clary sage plants from Bertie County, NC. Seven species were identified based on morphological features and by sequencing the ITS region of the rDNA. The most frequently recovered species were P. spinosum (5), P. sylvaticum (3), and P. irregulare (3). Seedling pathogenicity assays were performed on clary sage cultivars ‘English’ and ‘Early Selection’ by inoculating the embryonic plant root with a pathogen-colonized rice grain, and all isolates were pathogenic. Selected isolates also were pathogenic on seedlings grown in potting mix. All isolates were sensitive to mefenoxam at 100 µg/ml. To our knowledge, this is the first report of root rot of clary sage caused by Pythium spp. in North Carolina.