Dobrava hantavirus (DOBV) belongs to the genus Hantavirus of the family Bunyaviridae, and is carried by yellow necked and striped field mice (Apodemus flavicollis and Apodemus agrarius), respectively. The aim of this study was to detect and genetically characterize new DOBV strains in rodents captured in the Transdanubian region of Hungary. Rodent corpses were dissected and lung tissues were used for hantavirus detection by SYBR Green-based real-time RT-PCR using specific primers located in the S-segment of the virus genome. A total of 22 captured animals of the Apodemus species were tested for the presence of DOBV. Three out of the 22 mice were positive. Phylogenetic and molecular sequence analyses showed that Hungarian DOBVs were most closely related to those viruses detected from A. agrarius mice in Slovenia. Based on our new data from the region we concluded that extended reservoir studies would be necessary in the future.