In this study, we propose C. confusus, new species, an Andean slug of the genus Colosius Thomé, 1975, and a newly recognized pest of coffee and cultivated flowers from Colombia, Ecuador and Peru. We compare it with C. pulcher (Colosi, 1921), a poorly known species with which it has been confused. Our study is based on morphological analysis of a large number of specimens, including interceptions on cut-flowers and live plants by federal agricultural inspectors of the United States Department of Agriculture (USDA) and the Department of Homeland Security (DHS), and material from eight museum collections. Genetic diversity within C. confusus, n. sp. and C. pulcher is also analysed based on fragments of cytochrome oxidase I (COI), and 16S rRNA. They are differentiated by reproductive characters and genes studied. In C. confusus, n. sp., the phallus has a deep longitudinal groove from the base, near the retractor muscle, to its distal region, close to the papilla. In C. pulcher, there is an oval to rectangular swelling on the basal region of the phallus. Some important differences between these species are also found in the digitiform gland and bursa copulatrix. We describe, illustrate and discuss the color variation, morphological similarities, diagnostic characters and its variation, habitat and distribution for each species. Genetic diversity within C. confusus, n. sp., and C. pulcher is low. In order to analyze their relationship with C. propinquus (Colosi, 1921) (currently a junior synonym of C. pulcher) and C. lugubris (Colosi, 1921) (type-species of Colosius), fragments of COI, 16S, and 28S rRNA genes are also analyzed in a sample of these species. C. confusus, n. sp., is a distinct lineage within the genus Colosius. It is not a sister species of C. pulcher, which has C. propinquus as a sister species, here recognized as valid. Colosius confusus, n. sp., is closer to the clade that includes C. pulcher and C. propinquus than it is to C. lugubris. Based on the phylogenetic reconstruction, C. lugubris is sister to all the other Colosius, although additional studies are required to formally test phylogenetic placements and monophyly of the genus. Associated imports and number of interceptions per year of C. confusus, n. sp., by agricultural inspectors are also presented.