This study was focused on a special charophyte collected from Ya'an, Sichuan. Morphological observation showed that it had two-layer coronal, divided branchlets and no cortex. These were the features of Nitelleae. But there was another feature which hadn’t been reported in Nitelleae, papillary stipulodes, at the base of node and beneath the branchlets. The identical stipulodes were observed no matter in the fresh collected samples or in the laboratory cultured specimens or in the seedlings coming from the germinated oospores in the laboratory. Long time observation indicated that the stipulodes feature was stably inherited in this special charophyte. Further molecular phylogenetic analyses, which combined the 18s rDNA gene with the rbcL gene, demonstrated that new feature charophyte clustered with other species of Nitella as a single clade. Combining the morphological observation with the molecular analyses illustrated the new feature charophyte belonged to Nitella. Our research demonstrated that not only the Chareae but also the Nitelleae had stipulode. And the new feature charophyte was an important supplement to Nitella. New feature charophyte provided an evidence for the revision of the classification system of charophytes.