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With the end of the Civil War, the Union Army began to leave the island, which led to scores of freedmen leaving too, either following the Army for jobs, moving on to reclaimed plantations for wage jobs, or moving further inland. At the same time, the schools began to close, the barracks emptied, and the missionaries, once a sign of forward progression, left also. For the first time in six years, the freedmen who remained in Mitchelville were on their own.

In spite of these changes, it appears that Mitchelville was still an active village. An AMA teacher described Mitchelville in 1867:
“There are several large plantations upon which are small settlements, but the greater part of the colored population of the island are located a short distance from Hilton Head [meaning the old military base] at a place called Mitchelville. . . . It is an incorporated town, regularly laid out in streets and squares. About 1500 inhabitants, not a single white person. There are three churches – two Baptist, one Methodist, two schools which are taught by A.M.A. teachers.”

There were no whites living in Mitchelville since The Home, where AMA teachers had previously lived, had blown down during a storm in November 1867. What remained of the building, however, was still being used as a school. Although the military had left, taking jobs with them, many blacks turned to subsistence farming. Some formed collectives, joining together to rent large plantations from the government. Many of the freedmen were able to save their wages until they had the money to purchase land. However, many of the lands being planted by the freedmen were no longer available. Worse, many lands purchased by freedmen in good faith, were returned to their Southern owners, with the blacks divested of their interest.

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