The fungus Pyrenophora tritici-repentis causes tan spot, an important foliar disease of wheat, and can also infect the kernels, leading to the development of black point and red smudge on affected seeds. Production of the anthraquinones catenarin and emodin by P. tritici-repentis was evaluated in host tissues after inoculation of susceptible wheat genotypes. Catenarin is a bioactive red pigment hypothesized to cause the red smudge symptom; emodin has been classified as a diarrheagenic and genotoxic mycotoxin. Kernels harvested at maturity contained approximately 0.05μg catenarin and 0.06μg emodin per g tissue, whilst leaves harvested 7 days after inoculation contained 0.4μg catenarin per g tissue. No anthraquinones were detected in non-inoculated tissues. The detection of catenarin in kernels indicates that the pigment may cause the reddish discoloration associated with red smudge, while the identification of emodin suggests that P. tritici-repentis is a mycotoxigenic fungus. Catenarin also induced necrosis of leaves in a non-specific manner, suggesting that it contributes to non-specific symptom development by P. tritici-repentis. The pigment was also moderately active against some of the fungi associated with P. tritici-repentis during its saprophytic and parasitic phases of growth, indicating a possible role in the life strategy of the pathogen.