Genitalia morphology of a new gnorimoschemine micromoth (Lepidoptera, Gelechiidae, Gelechiinae, Gnorimoschemini) discovered in the Atacama Desert, northern Chile, fits the original description of Scrobipalpulopsis Povolný, 1987, a genus previously synonymized with Scrobipalpula Povolný, 1964. The generic assignment of the new species was assessed using a Bayesian phylogenetic analysis based on mitochondrial DNA sequences. The new species, the type species of Scrobipalpulopsis and another species recently transferred from this genus to Scrobipalpula were grouped in a monophyletic cluster distantly related to that of Scrobipalpula. Furthermore, an ancestral state reconstruction analysis suggested that the presence of two pairs of processes on the vinculum in the male genitalia represents a synapomorphy for the cluster of three species. Accordingly, the revalidation of Scrobipalpulopsisgen. rev. (type species Phthorimaea stirodes Meyrick, 1931) and the reinstated combination Scrobipalpulopsis lutescella (Clarke, 1934) comb. rev. are proposed. The micromoth Scrobipalpulopsis aguilaensissp. nov., whose larvae feed on inflorescences of the Chilean endemic Glandularia gynobasis (Verbenaceae), is described and illustrated. Genetic divergence with congenerics was found to be 2.5–4.4% (K2P). This discovery represents the first record of Scrobipalpulopsis from the Atacama Desert.