The Scrooby Congregation were English Protestant separatists who lived near Scrooby, on the outskirts of Bawtry, a small market town at the border of South Yorkshire, Lincolnshire and Nottinghamshire. In 1607/8 the Congregation emigrated to Netherlands in search of the freedom to worship as they chose. They founded the "English separatist church at Leiden", one of several English separatist groups in the Netherlands at the time.
Richard Clyfton was rector of Babworth, from 1605 under suspicion of nonconformity. Suspended, he continued to preach at Bawtry, near Scrooby though just over the county boundary in Yorkshire. From 1606 the congregation around Clyfton met in the house of William Brewster. This manor house has been identified as on the site of the old Scrooby Palace of the archbishops of York, though much of the older building had been demolished by then. In 1607 Clyfton was excommunicated; at this time he had already met William Bradford.
John Robinson from Sturton le Steeple, also in northern Nottinghamshire, had lost his church positions for his views and returned home by about the end of 1604; he made contact with separatist groups in Gainsborough, just over the eastern county boundary in Lincolnshire, as well as Scrooby. The minister at Gainsborough was John Smyth. In this way the two separatist churches were drawn together, with Robinson assuming authority in the Scrooby congregation alongside Clyfton after a process of ordination.