In this study, Cladonia yunnan was collected from the Fenghuang Mountains of southwest China in 2016. The algal photobiont of C. yunnan was successfully cultivated by dilution pipetting and direct methods under axenic conditions. Based on both morphological examination and phylogenetic analysis of molecular data, the results showed that: (1) the investigated photobiont was the only algae isolated from the C. yunnan, spherical or ellipsoidal, asexual reproduction, nonmotile unicellular green alga (cell size of approximately 2.5 to 6 μm), containing a parietal chloroplast with a central pyrenoid surrounded by starch. 3-5 cells enfold in a mucilaginous jelly. The cell nucleus was barely visible. (2) Based on our morphological characterization, the photobiont was similar to Coccomyxa subellipsoidea (freeliving). The photobiont is accordingly named Coccomyxa sp. YN with YN referring to the collection location (Yunnan, China). (3) Based on rbcL and ITS data, Coccomyxa sp. YN and C. subellipsoidea constituted one clade. ITS2 secondary structure were compared between Coccomyxa sp. YN and C. subellipsoidea. They have almost identical ITS2 secondary structure. Overall, this study reveals for the first time that Coccomyxa was the photobiont of Cladoniaceae. Coccomyxa sp. YN was closely related to C. subellipsoidea. Nonetheless, based on our morphological characterization, the Coccomyxa sp. YN may be modified in the lichenized state that is distinct from the closely related C. subellipsoidea. We speculate that photobionts may have evolved from freeliving algal cells.