in may 1866, joseph wilmer was elected as the second bishop of the diocese of louisiana, succeeding bishop (and general) leonidas polk, who had died during the siege of atlanta in 1864. he was consecrated as bishop in christ church, new orleans, on november 7, 1866, by presiding bishop john henry hopkins, as well as bishops william mercer green, richard hooker wilmer (his cousin), and charles todd quintard. during his episcopate, bishop wilmer grew the diocese, despite financial, flooding, and political troubles. during his first eight years, the number of congregations, church buildings, and communicants in the diocese more than doubled. wilmer died suddenly of apoplexy in new orleans on december 2, 1878. he was buried at green mount cemetery in baltimore, maryland.