The southwestern Andes of Peru harbors a hidden taxonomic diversity of Lepidoptera. Here a new leaf-mining species of Gracillariidae (Lepidoptera) is described,Phyllocnistis furcataVargas & Cerdeña,sp. nov., from a dry Andean valley of southern Peru, at 2400 m above sea level. The morphological aspects of adults (male and female) and the immature stages associated withBaccharis alnifoliaMeyen & Walp. (Asteraceae) are given, under optical microscopy and scanning electron microscopy. DNA barcodes show that its nearest neighbor is the Atlantic Forest speciesPhyllocnistis oureaBrito & Moreira, 2017 that feeds onBaccharis anomalaDC. The importance of morphological characters from immature stages for diagnosis among congeneric species is also discussed.Phyllocnistis furcatarepresents the fourth species ofPhyllocnistisZeller for Peru, and first record from the south of Peru for the genus.