John Jordan Morgan (1770 – July 29, 1849) was an American politician from New York.
Morgan was born in Queens County, New York, and attended the public schools.
Morgan was elected as a Jacksonian to the 23rd United States Congress to fill the vacancy caused by the resignation of Cornelius Van Wyck Lawrence and served from December 1, 1834, to March 3, 1835.
In February 1841, Morgan was appointed by President Martin Van Buren as Collector of the Port of New York to replace Jesse Hoyt who had been involved in the Swartwout-Hoyt scandal.
A month later, Morgan was removed by the new President William Henry Harrison who had defeated Van Buren for re-election.