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Southampton were founded at St. Mary's Church, on 21 November 1885 by members of the St. Mary's Church of England Young Men's Association.

St. Mary's Y.M.A., as they were usually referred to in the local press, played most of their early games on The Common where games were frequently interrupted by pedestrians insistent on exercising their right to roam. More important matches, such as cup games, were played either at the County Cricket Ground in Northlands Road or the Antelope Cricket Ground in St Mary's Road.

The club was originally known as St. Mary's Young Men's Association F.C. (usually abbreviated to "St. Mary's Y.M.A.") and then became simply St. Mary's F.C. in 1887–88, before adopting the name Southampton St. Mary's when the club joined the Southern League in 1894.

For the start of their League career, Saints signed several new players on professional contracts, including Charles Baker, Alf Littlehales and Lachie Thomson from Stoke and Fred Hollands from Millwall.After winning the Southern League title in 1896–97, the club became a limited company and was renamed Southampton F.C.

Southampton won the Southern League championship for three years running between 1897 and 1899 and again in 1901, 1903 and 1904. During this time, they moved to a newly built £10,000 stadium called The Dell, to the northwest of the city centre in 1898. Although they would spend the next 103 years there, the future was far from certain in those early days and the club had to rent the premises first before they could stump up the cash to buy the stadium in the early part of the 20th century. The club reached the first of their four FA Cup Finals in 1900. On that day, they went down 4–0 to Bury and two years later they would suffer a similar fate at the hands of Sheffield United as they were beaten 2–1 in a replay of the 1902 final.