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<i>Ageratina adenophora</i> is one of the most invasive weeds in China. Following an outbreak in Yunnan in the 1960s, <i>A. adenophora</i> has been spreading in Southwest China at tremendous speed. Previous research indicated <i>A. adenophora</i> contained many <i>Colletotrichum</i> species as endophytes. In this study, we investigated the diversity of <i>Colletotrichum</i> in healthy and diseased leaves of the invasive plant <i>A. adenophora</i> and several surrounding crops in Yunnan, Guangxi, and Guizhou provinces in China, and obtained over 1000 <i>Colletotrichum</i> strains. After preliminary delimitation using the internal transcribed spacer region (ITS) sequences, 44 representative strains were selected for further study. Their phylogenetic positions were determined by phylogenetic analyses using combined sequences of ITS, actin (<i>ACT</i>), chitin synthase (<i>CHS</i>-1), glyceraldehyde-3-phosphate dehydrogenase (<i>GAPDH</i>), and beta-tubulin (<i>TUB</i>2). Combined with morphological characteristics, 14 new <i>Colletotrichum</i> species were named as <i>C. adenophorae</i>, <i>C. analogum</i>, <i>C. cangyuanens</i><i>e</i>, <i>C. dimorphum</i>, <i>C. gracile</i>, <i>C. nanhuaens</i><i>e</i>, <i>C. nullisetosum</i>, <i>C. oblongisporum</i>, <i>C. parvisporum</i>, <i>C. robustum</i>, <i>C. simulanticitri</i>, <i>C. speciosum</i>, <i>C. subhenanense</i>, and <i>C. yunajiangens</i><i>e</i>.