The younger Basel line includes a Frankfurt sub-branch founded by the engraver Matthäus Merian the Elder (1593-1650), whose descendants became artists during the Baroque period and ran what became one of Europe's largest publishers in the 17th century.

The name probably derives from the office of Meier (meaning steward or estate manager); unlikely, however, is a speculated relationship to the community of Meria in Corsica or to an alleged Merian Abbey in the Archdiocese of Strasbourg, and the same is unlikely with reference to the Marioni nobility from Milan or to de Muriaux in the Bishopric of Basel.

The elder line stems from his son Theobald Merian (1465 – 1544), who went in 1480 as a seaman of Lüttelsdorf to Basel and later operated a sawmill on the right bank of the Rhine in Kleinbasel.

The younger line from Johann Petrus Merian (c.1468/1478 – after 1519) is thought to be related, as he was an episcopal steward who also came from Lüttelsdorf to Basel, but whether Theobald (the son) and Johann Petrus were brothers and both therefore sons of Theobald (the father) as tradition claims, is unproven.

Johann's elder brother Carl Gustav Merian was later elevated to the nobility by the Elector of Mainz and appointed to the Privy Council.