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He married, secondly, Mrs. Emily Marianne Forbes (née Ashworth), daughter of Maj.-Gen. Sir Charles Ashworth and Mary Anne Rooke, on 26 June 1858, in Trinity Chapel, Edinburgh, Scotland; Emily Forbes, at the time of the marriage, was the widow of Prof. Edward Forbes, the naturalist.
Hamilton's son, Charles Ashworth Hamilton, was the founder of Hamilton's Stores in Yellowstone National Park.