A number of insects, primarily Lepidoptera, cause damage to citrus in South Africa. A major limitation to the management and control of these pests is their correct identification. The aim of this study was to develop a database of gene sequences to aid in the identification of these Lepidoptera. Multiple specimens of 12 species were sequenced for the ∼650 bp of the cytochrome oxidase I gene. These sequence data were supplemented and validated using sequences available in public databases. Results showed that each species could be unambiguously identified, and neighbour-joining analysis based on K2P distances formed highly supported, distinct clusters for each species, i.e. the maximum intraspecific genetic distance was less than that of the minimum interspecific genetic distances. Thus, this data set provides a molecular means to successfully identify the most important Lepidoptera associated with citrus in South Africa.