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Thomas ap Catesby Jones (1790 - 1858) was a U.S. Navy officer during the War of 1812 and the Mexican-American War.

Jones was born in Westmoreland County, Virginia.

Thomas ap C. Jones began his naval career during the War of 1812, receiving honors for bravery at Lake Borgne, Louisiana, delaying the British before the Battle of New Orleans. In 1826, he signed a treaty with King Kamehameha III of the Sandwich Islands.

Commodore Jones commanded the United States Pacific Squadron from 1841 to 1844 and again from 1848 to 1850. In 1842, mistakenly thinking that war had begun between the U.S.A. and Mexico, he seized Monterey, California, for one day before returning control. In 1848, Jones arrived in Mazatlán just at the end of the Mexican-American War, maintaining order until he could transport those who had aided the United States in that war to Monterey. For the next two years, during the chaotic gold rush days, Jones provided a U.S. Navy presence in the San Francisco area while the United States debated what to do with the newly acquired California Territory.

In 1843, Jones returned a young deserter, Herman Melville, from the Sandwich Islands to the United States. Later, Melville modelled "Commodore J" in Moby-Dick and the commodore in White-Jacket after Jones. As Jones had a ship severely damaged in an attack by a whale in 1827, Moby-Dick may have been partially inspired by stories told of Jones.

In 1850, in a politically-charged court-martial shortly after White-Jacket was published, Jones was found guilty on three counts mostly related to "oppression" of junior officers and relieved of command for two and a half years. In 1853, President Millard Fillmore reinstated him, and, in 1858, the United States Congress restored his pay.

Jones' brother, Roger Jones, was Adjutant General of the United States Army from 1824 to 1852.

Note: "ap" is a Welsh indication for "son of". Thomas ap Catesby Jones is Thomas, son of Catesby Jones.

• Gene A. Smith, Thomas ap Catesby Jones, Commodore of Manifest Destiny (Annapolis, MD: Naval Institute Press, 2000) ISBN 1-55750-848-8