During the field studies, a Translucidithyrium-like taxon was collected in Xishuangbanna of Yunnan Province, during an investigation into the diversity of microfungi in the southwest of China. Morphological observations and phylogenetic analysis of combined LSU and ITS sequences revealed that the new taxon is a member of the genus Translucidithyrium and it is distinct from other species. Therefore, Translucidithyrium chinense sp. nov. is introduced here. The Maximum Clade Credibility (MCC) tree from LSU rDNA of Translucidithyrium and related species indicated the divergence time of existing and new species of Translucidithyrium was crown age at 16 (4–33) Mya. Combining the estimated divergence time, paleoecology and plate tectonic movements with the corresponding geological time scale, we proposed a hypothesis that the speciation (estimated divergence time) of T. chinense was earlier than T. thailandicum. Our findings provided new insights into the species of Translucidithyrium about ecological adaptation and speciation in two separate areas.