The industrial chicory is cultivated for fructan extraction from their roots, food which promotes human health. In Chile the crop was introduced in 2006 and from the beginning showed an undescribed disease, causing significant damages to the root and yield losses up to 31%. Besides the industrial problems in fructan extraction. The objectives were to describe and identify the causing agent and to assess the incidence, severity and pathogenicity. This investigation was conducted between 2009 and 2013. The symptoms on the crown and upper taproot started as small, dark, firm, sunken lesions, and then turned from brownish to black. Root cavities lacked fungal signs and covered the entire root up to 20% of the analyzed plants at harvest. In 2009 the disease incidence occurred on 39% of the sampled plants. From the infected roots, a fungus was consistently isolated on acidified PDA and water agar. The pathogenicity tests showed that the pathogen caused rot on detached roots, entire roots, potted plants and plants growing on inoculated soil. The fungus was reisolated from the symptomatic tissues, confirming Koch’s postulates. On the basis of its morphological characteristics on oatmeal agar, the presence of metabolite ‘E’ on malt agar and the pathogenicity tests, the isolates were identified as <i>Boeremia exigua</i> var. <i>exigua.</i> To our knowledge this is the first report of <i>B. exigua</i> var. <i>exigua</i> in industrial chicory in Chile.