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<i>Castilleja tenuiflora</i> is a native perennial plant used in traditional Mexican medicine. In June 2022, leaf blight symptoms were observed in a wild population of <i>C. tenuiflora</i> plants. Disease incidence was 80% and disease intensity reached up to 5% of the leaf area. Currently, there are no reports of pathogens causing leaf blight in this plant; therefore, this work aimed to identify the fungi responsible for the disease. The fungi recovered from the diseased tissue were characterized by means of pathogenicity tests and cultural, morphological, and molecular characterization. The information obtained revealed that <i>Alternaria alternata</i> and <i>Alternaria gossypina</i> are the pathogens responsible for the disease. This is the first report implicating species of <i>Alternaria</i> in causing leaf blight of <i>C. tenuiflora</i> in Mexico, as well as the first report of <i>Alternaria gossypina</i> also in Mexico. These pathogens may threaten the in situ conservation of native <i>C. tenuiflora</i> populations and limit their in vitro propagation. Future research lines should focus on determining the effect of these pathogens on metabolite production.