Houblon was the eldest son of merchant Jacob Houblon and his wife Susannah Archer of Hallingbury Place in Great Hallingbury. His younger sisters were Maria Houblon (wife of Rev. Ambrose Alexander Cotton) and Letitia Houblon (wife of Frederic Louis von Feilitzsch).[1]
He married Mary Ann Bramston, the daughter of Thomas Berney Bramston of Skreens and sister of Thomas Gardiner Bramston, both MPs for Essex. Together, Mary Ann and John were the parents of ten sons and three daughters, including:[5]
John Archer-Houblon (1803–1891), who married Anne Whitley Deans Dundas, eldest daughter of Adm. Sir James Whitley Deans Dundas and Janet Dundas (only daughter and heir of Lord Amesbury), in 1829. After her death in 1847, he married Georgina Anne Oswald, a daughter of Gen.Sir John Oswald.[1]
Jacob William Houblon (1805–1819), who died young.[1]
Charles Archer-Houblon Eyre (1806–1886), who married Mary Anne Popham, a daughter of Gen. Leyborne Popham of Littlecote House, in 1835. After her death in 1855, he married Louisa Charlotte Randolph, a daughter of the Rev. Thomas Randolph, Rector of Much Hadham in 1858.[1]
Thomas Archer-Houblon (1808–1874), Rector of Catmore and Peasemore who married Eleanor Deedes, daughter of the Rev. John Deeds, Rector of Willingdale, in 1839.[1]
Susanna Laetitia Archer-Houblon (1810–1846)
Mary Anne Archer-Houblon (1811–1896), who married William Forbes, eldest son of the Hon. John Hay Forbes, Lord Medwyn, in 1842.[1]
Harriet Archer-Houblon (1812–1896), who died unmarried.[1]
Richard Archer-Houblon (1814–1894), who married his cousin, Anne Maria Cotton, youngest daughter of the Rev. Alexander A. Cotton, Rector of Girton Co., in 1853.[1]