We describe a new species of Cuphodes Meyrick, 1897 (Lepidoptera: Gracillariidae) from South Africa, C. spermotrophus sp. nov., reared from fruits of Rhamnus prinoides L'Hér. (Rhamnaceae). This represents the first confirmed record of a seed-feeding Gracillariidae species from the African continent. The new species is distinguished from all known congeners by external morphology and male and female genitalia. Molecular data (COI barcode) confirm its distinctiveness and support its placement within Cuphodes. We provide diagnostic characters, illustrations of the adult and genitalia, and notes on its biology and host association. The discovery of this species expands the known feeding habits of Cuphodes, previously thought to include only leaf-mining species, and highlights the still largely unexplored trophic diversity of African Gracillariidae.