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Muhlenberg was the brother of Frederick and Peter Muhlenberg, father of Henry A. P. Muhlenberg and Frederick Augustus Hall Muhlenberg, a physician, who was the father of Frederick Augustus Muhlenberg, the first president of Muhlenberg College.
In 1862 the presidency of Girard College, Philadelphia, was offered to him, and in 1869 the professorship of Latin in Muhlenberg College, Allentown, Pennsylvania, but he declined both.