Jakob Christoph Blarer von Wartensee (11 May 1542 – 18 April 1608) was a Bishop of Basel and a leader in the Counter-Reformation in the region around Basel.
He was born at Rosenberg Castle, the son of William, Prince-abbot of St. Gall and upper Vogt of Rosenberg, and Helen of Hallwyl. Between 1557–59 he was a student at Freiburg under the humanist Heinrich Glarean. In 1555 he was appointed to the Cathedral of Constance. He became a canon in 1559, and an archdeacon in 1570. In 1561 he moved to Basel's cathedral. He was unanimously elected Bishop of Basel on 22 June 1575, and on 4 May 1576 this election was confirmed by Pope Gregory XIII. He was ordained on 10 February 1577 and was granted an Imperial investiture on 15 November 1577.
Starting in 1576, he was planning an alliance with the catholic cantons in order to restore the power of the his Bishopric of Basel. Basel had converted to the Reformation during the first half of the 16th century. After costly negotiations and with the help of Ludwig Pfyffer von Altishofen and the nuncios Ninguarda Feliciano and Giovanni Francesco Bonomi, a catholic mutual assistance pact was signed on 28 September 1579 in Lucerne and all parties swore to uphold the pact on 11 January 1580 in Porrentruy. This provided a base of support for Blarer's goals; the Catholic renewal of the diocese's subjects, to prevent further removal of existing Burgrecht (rights between a town and the surrounding villages), the recovery of former Catholic dominions within and outside the city of Basel as well as restitution of cathedral's property.