Potato mop-top virus (PMTV) is an important pathogen of potato (Solanum tuberosum L.), occurring in Northern Europe, North and South America, and Asia, that significantly reduces potato production (Santala et al., 2010). PMTV is transmitted by spores of Spongospora subterranea f. sp. subterranea (Sss), the causal agent of powdery scab of potato (Jones and Harrison, 1969). During the summer season of 2012, native potato (S. tuberosum L. ssp. tuberosum) leaves showing virus-like symptoms were collected on several points within the Chiloé Archipelago (Chiloé Province, in the south of Chile), one of the centers of origin and diversity of cultivated potatoes (Montaldo, 1984). The presence and identity of viruses in the samples were determined through next generation high throughput sequencing (Solexa-Illumina) followed by assembly of viral small RNAs (vsRNAs) to reference plant virus genomes. The plant material used for the construction of the sRNA library corresponded to pools of symptomatic leaves sampled in the Archipelago. This analysis revealed that PMTV was infecting native potatoes in Chiloé, since the assembled contigs covered a 77.3, 76.8 and 68.0% of PMTV RNA1 (Reference sequence: NC_003723.1), RNA2 (Reference sequence: NC_003725.1) and RNA3 (Reference sequence: NC_003724.1), respectively. Subsequently, three farms growing native potatoes (local varieties Michuñe negra, Michuñe roja and Clavela lisa) with symptoms associated with PMTV infections were identified in Puqueldón (Lemuy Island, Chiloé Province ) during the summers of 2013 and 2014. Disease symptoms observed included stunting of stems, shortening of internodes, and mosaic patterns (V-shaped) on leaves, but necrotic symptoms on the surface or the flesh of tubers were not observed. To detect PMTV,total nucleic acid was extracted from three symptomatic plants each year and tested by reverse transcription (RT)-PCR using two sets of primers. In all samples analyzed, primer set C819/H360, targeting the coat protein (CP) gene in RNA3, yielded an amplicon of 460 bp (Xu et al., 2004). Primer set pmtF4/pmtR4 amplified a fragment of 417 bp from the second gene of the triple gene block (TGB2) in RNA2 (Xu et al., 2004). PCR products were directly sequenced (GenBank Accession Nos. KT267163 and KT267164). BLAST analysis showed that the amplicons were 99 to 100% identical to most of the CP or TGB2 sequences from several PMTV isolates from Europe and the United States. A double antibody sandwich enzyme-linked immunosorbent assay (DAS-ELISA, Bioreba AG) on the same symptomatic potato leaf samples confirmed the presence of the virus in all cases. To our knowledge this is the first report of PMTV in Chile. However, the powdery scab pathogen, Sss, is widespread in the potato production areas near Chiloé Province. These results provide important and cautionary information to be considered by programs managing seed tuber production and plant quarantine for potato pathogens in Chile.