The church was begun in 1857 and completed in 1864. The construction was sponsored by the wealthy Basel businessman Christoph Merian and his wife Margarethe Burckhardt-Merian.  They were both laid to rest in black marble sarcophagi in the crypt below the church's main floor.
The Merians also founded the Christoph-Merian-Stiftung.
Today's congregation forms part of the Evangelical-Reformed Church of the Canton Basel-Stadt.
Today the church is home of the first Swiss "OpenChurch" or Offene Kirche Elisabethen].  The Offene Kirche Elisabethen caters to the spiritual, cultural and social needs of urban people of all backgrounds: Businesspeople, shoppers, tourists, asylum seekers, working poor, minorities, homeless etc.
Schöpfungsfeier (service with blessing of the human-animal relation), Heilungsfeiern (weekly and trimesterly healing-/blessing services for people in need and sorrow) and their gender aware spiritual practice ("Women at the altar", "Lesbian-Gay-Biseuexual-Transgender"-Community[permanent dead link]).
Nearly 50'000 people visit the church per year.
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