Gunther was a scion of the Ekkeharding noble family first recorded around Naumburg, which may be affiliated with the Ottonian dynasty.
In 962, he was already regarded as a margrave in the newly created Diocese of Magdeburg, alongside Count Wigger of Bilstein and Wigbert.
He was appointed to the newly created Merseburger march by Emperor Otto I following the death of Margrave Gero the Great in 965, after which the Marca Geronis was split in several smaller parts.
Gunther nevertheless became reconciled with Otto II and after Thietmar's death in 979 was reinstalled as margrave.
He joined Otto's campaign in Calabria in 982 and died there in the Battle of Stilo against the Saracens.