The genus Paraphoma (Phaeosphaeriaceae) consists of a small number of saprotrophic and phytopathogenic species that cause various diseases (root and crown rot, leaf spots) in cultivated and wild plants. Some Paraphoma spp. have been known to produce biologically active secondary metabolites. In this study, Paraphoma fungi isolated from diseased leaves of Cirsium arvense and C. pendulum were characterized using a polyphasic approach combining the study of morphological features, secondary metabolite profiling, and multilocus phylogenetics using the ITS region along with partial TEF1-α and TUB2 gene sequences. As a result, two new species (Paraphoma rubrobrunnea sp. nov. and Paraphoma cirsii sp. nov.) were described and then characterized. The pathogenicity of P. rubrobrunnea toward its host C. arvense was proved, while P. cirsii exhibited endophytic growth in leaves of aboveground shoots of this plant. Paraphaeosphaeride D and two carbocyclic aspochalasins (16-hydroxymethylaspergillin PZ and 19-hydroxyl-19,20-dihydrophomacin C) were isolated from liquid cultures of P. rubrobrunnea as its major metabolites. A main metabolite of P. cirsii was phaeosphaeride A. Furthermore, detectable amounts (