The Eucalyptus Weevil, generally referred to as Gonipterus scutellatus Gyllenhal, 1833 is a significant pest of Eucalyptus species in Africa, America, Europe and New Zealand. It has recently become a pest of Eucalyptus globulus plantations in Western Australia, despite the presence there of the mymarid egg‐parasitoid Anaphes nitens (Girault). Recent taxonomic study has indicated G. scutellatus to comprise a complex of cryptic species, obscuring the identity of the various pest populations of the weevil in the world. We examined (1) whether the apparent cryptic species identifiable on genital differences have a genetic basis; (2) the distribution of these species; and (3) the origin of the population in Western Australia. We studied specimens from across the distribution range of Eucalyptus Weevil in Australia and obtained sequences of three genes from them: cytochrome oxidase I mtDNA, elongation‐factor 1‐α nuclear DNA and 18s rDNA. The cladogram of COI haplotypes resolved 10 well supported clades fully corresponding with genital‐morphologically distinct species, eight of them constituting a monophyletic G. scutellatus complex. Only four of these species proved to be described, as G. balteatusLea, 1897G. platensis (Marelli, 1926), G. pulverulentusLea, 1897 and G. scutellatus Gyllenhal, 1833. The pest species in the world were found to be G. platensis (New Zealand, America, western Europe), G. pulverulentus (eastern South America) and an undescribed species (Africa, France, Italy). The population of G. platensis in Western Australia showed little genetic variation and is indicated to be a recent introduction from Tasmania. The discrimination of the cryptic species of the G. scutellatus complex enables improvements in the management of the pest species in terms of biological control and plantation practices. Our study highlights the critical importance of proper taxonomic studies underpinning biocontrol programs.