The garlic (Allium sativum L.) cultivated in the O’Higgins Region, the main garlic-producing area in Chile, is the commercial type known as pink garlic, which presents a low yield and a high prevalence of symptoms associated with viral infections. A survey was carried out in the three localities of the region that cultivate this vegetable to identify, by reverse transcription polymerase chain reaction (RT-PCR), the presence of Onion yellow dwarf virus (OYDV) and Leek yellow stripe virus (LYSV). The results indicated a prevalence of 99.5% and 54.0% respectively. In addition, a molecular and phylogenetic analysis of the amplified genome fragments for both viruses was performed. Using the nucleotide BLAST (BLASTn) tool, nucleotide sequences were compared with sequences available in the National Center for Biotechnology Information (NCBI) database. The Chilean sequences were aligned with complete sequences available at NCBI and a phylogenetic tree was constructed using the Neighbor-Joining method. The results showed genetic variability among Chilean isolates.