During investigation of pathogenic Alternaria in China, nine Alternaria isolates were obtained from two Caryophyllaceae plants. Based on morphological and multilocus phylogenetic approaches and pathogenicity tests, three pathogenic species of Alternaria including two new species and a new record in China were identified. Phylogenetically, the present species were confirmed and grouped within two clades out of three in section Gypsophilae: clade I (Alternaria hispanica sp. nov. and A. vaccariae) and clade II (Alternaria barbata sp. nov.). Morphological comparison was conducted between the two new species and their closely related ones which verified the phylogenetic results. The two novel species were described and illustrated here.