Territories of the dominant noble houses in Swabia and Upper Burgundy around 1200; Zähringen possessions shown in green
The earliest known ancestor of the family was one Berthold, Count in the Breisgau (d. 982), who was first mentioned in 962. In view of his name, he may have been related to the Alemannic Ahalolfing dynasty. Berthold's great-grandson, Berthold I of Zähringen (c. 1000 – 6 November 1078), held several lordships (Herrschaften) in the Breisgau, in Thurgau, Ortenau, and Baar. By his mother, he was related to the rising Hohenstaufen family.
Emperor Henry III had promised his liensman Berthold I of Zähringen the Duchy of Swabia, but this was not fulfilled, as upon Henry's death, his widow Agnes of Poitou appointed Count Rudolf of Rheinfelden to the position of Duke of Swabia in 1057. In compensation, Berthold was made Duke of Carinthia and Margrave of Verona in 1061. However, this dignity was only a titular one, and Berthold subsequently lost it when, in the course of the Investiture Controversy, he joined the rising of his former rival Rudolf of Rheinfelden against German king Henry IV in 1073.
Berthold's son Berthold II, who like his father fought against Henry IV, inherited a lot of the lands of Rudolf's son Count Berthold of Rheinfelden in 1090 (though not his comital title, which stayed with the family von Wetter-Rheinfelden). In 1092, Berthold II was elected Duke of Swabia against Frederick I of Hohenstaufen. In 1098, he reconciled with Frederick, renounced all claims to Swabia and instead concentrated on his possessions in the Breisgau region, assuming the title of Duke of Zähringen. He was succeeded in turn by his sons,
Berthold III (d. 1122) and Conrad (d. 1152).
In 1127, upon the assassination of his nephew Count William III, Conrad claimed the inheritance of the County of Burgundy against Count Renaud III of Mâcon. Renaud prevailed, though he had to cede large parts of the eastern Transjuranian lands to Conrad, who thereupon was appointed by Emperor Lothair III as a "rector" of the Imperial Kingdom of Arles or Burgundy. This office was confirmed in 1152 and held by the Zähringen dukes until 1218, hence they are sometimes called "Dukes of Burgundy", although the existing Duchy of Burgundy was not an Imperial but a French fief. Duke Berthold IV (d. 1186), who followed his father Conrad and founded the Swiss city of Fryburg (today's Fribourg-Freiburg) in 1157, spent much of his time in Italy in the train of Emperor Frederick I Barbarossa.
His son and successor, Berthold V, showed his prowess by reducing the Burgundian nobles to order. This latter duke was the founder of the city of Bern (1191), and when he died in February 1218, the ducal line of the Zähringen family became extinct. Among other titles, the Zähringen family acted as Reichsvogt of the Zürichgau area.
After the extinction of the ducal line in 1218, much of their extensive territory in the Breisgau and modern-day Switzerland returned to the crown, except for their allodial titles, which were divided between the Counts of Urach (who subsequent called themselves the Counts of Freiburg) and the Counts of Kyburg, both of whom had married sisters of Berthold V. Less than fifty years later, the Kyburgs died out and large portions of their domains were inherited by the House of Habsburg. Bern achieved the status of a free imperial city, whereas other cities such as Fribourg-Freiburg only obtained the same status later in history.