A new shallow-water gorgonian coral species in the family Acanthogorgiidae, Paraplexaura binyuani sp. nov., is described from a specimen collected at Huaguang Atoll in the South China Sea at a depth of 22 m. The new species is distinguished from its congeners by abundant polyp sclerites, predominantly flattened rods, and by the coenenchyme bearing numerous large spindles reaching up to 0.6 mm in length, which are approximately two to three times longer than those reported for most described species of Paraplexaura. Phylogenomic analyses based on ultraconserved elements (UCEs) recover Paraplexaura as monophyletic and place P. binyuani sp. nov. as sister to P. cryptotheca, consistent with its morphological distinctiveness and supporting its recognition as a separate species.