Deformed wing virus (DWV) is one of the most common viruses affecting honey bee specimens. Although the presence of DWV has been reported in many countries, there is no data of the current situation in Chile. In this report, we detected the presence of DWV in apiaries from two different locations in central Chile. Furthermore, the genome of a Chilean DWV isolate was completely sequenced. This is the first report of the presence of a honey bee virus in Chile.