He was the son of Catherine Alexander (Robinson) and Alexander Slidell Mackenzie, both of whom were natives of New York City. His father was a well-known naval officer whose career had been surrounded in controversy (see USS Somers (1842)); his uncles included William Alexander Duer, John Slidell, and Matthew C. Perry. By the time of his birth, his parents had purchased a farm on the Hudson between Tarrytown and Sing Sing. His father died suddenly September 13, 1848, at his residence, near Tarrytown, N.Y., of heart disease.