The southwestern Andes of Peru harbors a hidden taxonomic diversity of Lepidoptera. Here a new leafmining species of Gracillariidae (Lepidoptera) is described, Phyllocnistis furcata Vargas & 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 with Baccharis alnifolia Meyen & Walp. (Asteraceae) are given, under optical microscopy and scanning electron microscopy. DNA barcodes show that its nearest neighbor is the Atlantic Forest species Phyllocnistis ourea Brito & Moreira, 2017 that feeds on Baccharis anomala DC. The importance of morphological characters from immature stages for diagnosis among congeneric species is also discussed. Phyllocnistis furcata represents the fourth species of Phyllocnistis Zeller for Peru, and first record from the south of Peru for the genus.