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<i>Diaporthe</i> species are endophytes, pathogens, and saprobes with a wide host range worldwide. However, little is known about endophytic <i>Diaporthe</i> species associated with <i>Morinda officinalis</i>. In the present study, 48 endophytic <i>Diaporthe</i> isolates were obtained from cultivated <i>M. officinalis</i> in Deqing, Guangdong Province, China. The nuclear ribosomal internal transcribed spacer (ITS), partial sequences of translation elongation factor 1-α (<i>tef1-α</i>), partial calmodulin (<i>cal</i>), histone H3 (<i>his</i>), and Beta-tubulin (<i>β-tubulin</i>) gene regions were sequenced and employed to construct phylogenetic trees. Based on morphology and combined multigene phylogeny, 12 <i>Diaporthe</i> species were identified, including five new species of <i>Diaporthe longiconidialis</i>, <i>D. megabiguttulata</i>, <i>D. morindendophytica</i>, <i>D. morindae</i>, and <i>D. zhaoqingensis</i>. This is the first report of <i>Diaporthe chongqingensis</i>, <i>D. guangxiensis</i>, <i>D. heliconiae</i>, <i>D. siamensis</i>, <i>D. unshiuensis</i>, and <i>D. xishuangbanica</i> on <i>M. officinalis</i>. This study provides the first intensive study of endophytic <i>Diaporthe</i> species on <i>M. officinalis</i> in China. These results will improve the current knowledge of <i>Diaporthe</i> species associated with this traditional medicinal plant. Furthermore, results from this study will help to understand the potential pathogens and biocontrol agents from <i>M. officinalis</i> and to develop a disease management platform.