Capillaria Moravec, 1987, is a genus of thin, threadlike roundworms infecting various hosts, including fishes. Fifteen species have been described from freshwater, brackish-water and marine fishes, primarily based on morphological characters. However, species identification remains challenging, and no molecular information is currently available for previously described Capillaria species. Utilizing morphological, scanning electron microscopy, and molecular evidence, we describe Capillaria (Procapillaria) nubthaiensis Chan, 2025 as a new species of capillariid infecting the commercially important fish Scomberomorus commerson from the Gulf of Thailand. Examination of 30 male and 30 female specimens revealed key morphological features distinguishing Capillaria nubthaiensis sp. nov. from other members of Capillaria (Procapillaria). These morphological characters include a unique female vulva that appears slightly protruding and forms a ‘knob-like’ shape appendage and a small papilla near the base of each male lobe with another pair of small papillae near the anus. Molecular phylogenies obtained from the nuclear 18S ribosomal RNA and the mitochondrial cytochrome c oxidase subunit I genes also support the distinction from other species in the family Capillariidae. The discovery of C. nubthaiensis sp. nov. represents the first record of a Capillaria species infecting S. commerson, and it is also the first to be recorded in Thailand’s marine waters. Alongside molecular information, this study contributes vital information beneficial for the taxonomy and biodiversity of capillariids in marine fishes.