Description of the dataset This dataset contains morphological and genetic information of Aphrastura populations in different sample sites in Chile and Argentina. This dataset was analysed in: Rozzi R, Quilodrán CS, Botero-Delgadillo E, Napolitano C, Torres-Mura JC, Barroso O, Crego RD, Bravo C, Ippi S, Quirici V, Mackenzie R, Suazo CG, Rivero-de-Aguilar J, Goffinet B, Kempenaers B, Poulin E and RA Vásquez. 2022. The Subantarctic Rayadito (Aphrastura subantarctica), a new bird species on the southernmost islands of the Americas. Scientific Reports. There are three files: Subantarctic_Rayadito_Morphology.txt: morphological information used for differentiating Aphrastura subantarctica from Aphrastura spinicauda. The former was sampled in the Diego Ramirez archipelago. The date of sampling is included in the last column. Subantarctic_Rayadito_Microsatellite.txt: all captured and genotyped adults from five populations. The band (ring) number is used as an ID for each individual bird. The matrix includes information regarding the locality of origin (MA: Manquehue; BA: Bariloche; TF: Tierra del Fuego; NI: Navarino Island; DR: Diego Ramírez Archipelago), and allele size (number of repeats) at 12 polymorphic microsatellite loci. Subantarctic_Rayadito_mtDNA.nex: mtDNA information for all Aphrastura individuals sequenced and used in our analysis. The labels denote the code number and location for each individual (DR: Diego Ramirez Archipelago; CH: Cape Horn Island ; Navarino : Navarino Island; TdelFuego : Tierra del Fuego; PtoNatales : Puerto Natales ; ElChalten : El Chalten; CalTortel : Caleta Tortel ; Coihayque : Coihayque ; Chaiten : Chaiten ; LosAlerces : Los Alerces ; Chiloe : Chiloé Island ; IslaMocha : Mocha Island ; Curacautin : Curacautin ; Rinihue : Rinihue ; Epulauquen : Epu Lauquen ; Constitucion : Constitución ; Manquehue : Manquehue ; FrayJorge : Fray Jorge National Park). Acknowledgments This study was funded with Grants from the Sub-Antarctic Biocultural Conservation Program of the University of North Texas, University of Magallanes, the Cape Horn International Center (ANID CHIC-FB210018), the Institute of Ecology and Biodiversity of Chile (CONICYT PFB-23), and the Patagonia Mar y Tierra Working Group (The Pew Charitable Trust - Chile). We thank the support of the Omora Foundation, and FONDECYT 1140548 to RAV. C.N. thank support from ANID PAI 77190064, and ANID/BASAL FB210006. CSQ acknowledges support from the Swiss National Science Foundation (N° P400PB_183930 and P5R5PB_203169). We are grateful to Sylvia Kuhn and Alexander Girg from the Max Planck Institute for Ornithology for help in the laboratory, and to Jaime A. Cursach and Maximiliano Daigre during fieldwork and ornithological records in Gonzalo Island. Fieldwork in protected areas was possible thanks to people from Parque Nacional Bosque Fray Jorge, Minera Los Pelambres, Estación Biológica Senda Darwin, Parque Nacional Nahuel Huapi, and Parque Natural Karukinka. We also express our gratitude for logistical and personnel support from the 3rd Naval Zone of the Chilean Navy.