Cryphodera guangdongensis n. sp. was collected from the soil and roots of Schima superba in Guangdong province, China. The new species is characterised by having a nearly spherical female, with dimensions of length × width = 532.3 (423.8–675.3) × 295.6 (160.0–381.2) μm, stylet length of 35.7 (31.1–42.1) μm, protruding vulval lips, a vulval slit measuring 54.2 (47.4–58.9) μm, an area between the vulva and anus that is flat to concave, and a vulva–anus distance 49.3 (41.1–57.6) μm. The male features two lip annules, a stylet length of 31.7 (27.4–34.8) μm and basal knobs that are slightly projecting anteriorly, while lateral field is areolated with three incisures and spicules length of 27.1 (23.7–31.0) μm. The second stage juvenile is characterised by a body length of 506.1 (441.8–564.4) μm long, two to three lip annules, a stylet length 31.2 (29.7–33.2) μm which is well developed, basal knobs projecting anteriorly, a lateral field that is areolate with three incisures, and a narrow rounded tail measuring 63.2 (54.2–71.3) μm long, with a hyaline region of 35.6 (27.4–56.6) μm long that is longer than the stylet. Based on morphology and morphometrics, the new species is closely related to C. sinensis and C. japonicum within the genus Cryphodera. The phylogenetic trees constructed based on the ITS-rRNA, 28S-rRNA D2–D3 region, and the partial COI gene sequences indicate that the new species clusters with other Cryphodera species but maintains in a separated subgroup. A key to the species of the genus Cryphodera is also provided in this study.