In June 1838 he was ordered to command , attached to Commander Charles Wilkes's exploring expedition, second in command overall. After strenuous service in the Antarctic, the South Seas, and along the coast of North America, "Peacock" was wrecked 18 July 1841 while attempting to cross the bar and enter the Columbia River on Wilkes' orders. Commander Hudson made every effort to free his ship but was forced to leave her, saving all his men and the scientific papers.