Chrysosplenium guangxiense H.G.Ye & Gui C.Zhang was first described as a new species in 1994 but later synonymized in the Flora of China treatment with C. glossophyllum H.Hara. Plastid genomes and nrDNA sequences were used to infer the phylogenetic relationships of selected taxa in Chrysosplenium. Our phylogenetic analyses revealed that C. guangxiense belongs to sect. Alternifolia, is closely related to Chrysosplenium hydrocotylifolium H.Lév. & Vaniot but distant from C. glossophyllum. Morphologically, C. guangxiense could be easily distinguished from C. glossophyllum by having robust rhizomes, basal leaves with a long cuneate base and fewer teeth in the margin, curled sepal margins, and red, larger seeds. It could also be easily distinguished from C. hydrocotylifolium by possessing long elliptic leaves and a long cuneate leaf base. Along with the phylogenetic studies, the complete plastid genome of C. guangxiense was also reported. The plastid genome was 154,004 bp in length and comprised two inverted repeats (IRs) of 28,120 bp, separated by a large single-copy of 80,646 bp and a small single-copy of 17,118 bp. A total of 111 functional genes were discovered, comprising 78 protein-coding genes, 29 tRNA genes, and four rRNA genes. Based on assessment of morphological and molecular data Chrysosplenium guangxiense H.G.Ye & Gui C.Zhang is resurrected from C. glossophyllum H.Hara at species level. A global conservation assessment classifies C. guangxiense as Vulnerable (VU).