Though the Counts of Ortenburg—formerly Ortenberg—emerged in the 12th century as a cadet branch of the Rhenish House of Sponheim (Spanheim) who then ruled over the Duchy of Carinthia, an affiliation with the Carinthian Ortenburger comital family is unverifiable.

When his brother Engelbert III died without heirs in 1173 he could unite a significant number of territories under his rule and confirmed his independence when the Bavarian ducal title passed to the House of Wittelsbach in 1180.

Rapoto's II descendants, however, soon entered into fierce conflicts with the neighbouring Bishops of Passau and also with the mighty Austrian House of Babenberg.

Meanwhile, the county had fallen under the influence of the Wittelsbach Bavaria-Landshut duchy, and also sided with Duke Albert IV of Bavaria-Munich in the 1503 Landshut War of Succession.

The county remained a Lutheran enclave within the mainly Catholic Bavarian lands and became a refuge for expellees during the Thirty Years' War.