Promoted enseigne de vaisseau in 1830, he participated in the French expedition against Algiers and the forcing of the Tagus in 1831. In 1832 he served aboard Ducreuse during the blockade of the Dutch coast in the Belgian War of Independance. He was promoted lieutenant de vaisseau in 1834.
In 1843, he assumed command of the corvette Victorieuse on the China and India Seas station, and took part in an expedition to explore the Yellow Sea. On 25 April 1847 Victorieuse and Gloire (capitaine de vaisseau Augustin de Lapierre), which had been sent to Da Nang (Tourane) to negotiate for the release of two French Catholic missionaries, were attacked without warning by several Vietnamese vessels, in an incident known as the Bombardment of Da Nang. The two French ships fought back, and with their superior armament rapidly destroyed their attackers. In July 1847 Victorieuse ran aground on the coast of Korea, but Rigault de Genouilly was exonerated from blame by a court of enquiry.
He was promoted captaine de vaisseau in July 1848, and served on a commission charged with studying the defences of Havre. He then became chef de cabinet of the navy minister Joseph Grégoire Cazy. Between 1849 and 1851 he was captain successively of the frigate Vauban and of Charlemagne, the first screw-driven French warship. He conducted extensive tests on Charlemagne, for which he received the thanks of the admiralty.
In 1857 Rigault de Genouilly sailed on Némésis to join the naval armada assembled by Admiral Léonard Charner for the Second Opium War, and was placed in command of the French naval division. During the campaign he took part in the blockade of Macau and captured the city of Canton. After this success he served at the capture of the Peiho forts and accompanied the Anglo-French expedition to Tientsin.
The allies expected an easy victory, but the war did not at first go as planned. Vietnamese resistance was more stubborn than had been expected, and the French and Spanish found themselves besieged in Da Nang by a Vietnamese army under the command of Nguyen Tri Phuong. The Siege of Đà Nẵng lasted for nearly three years, and although there was little fighting disease took a heavy toll of the allied expedition. The siege eventually ended with the unopposed evacuation of the French garrison in March 1860.
Shortly after his capture of Da Nang, Rigault de Genouilly cast around for somewhere else to strike the Vietnamese. In January 1859 he proposed to the navy ministry an expedition against Saigon in Cochinchina, a city of considerable strategic significance as a source of food for the Vietnamese army. The expedition was approved, and in early February, leaving capitaine de vaisseau Thoyon at Da Nang with a small French garrison, Rigault de Genouilly sailed south for Saigon with a powerful naval flotilla and a Franco-Spanish landing force. On 17 February 1859, after forcing the river defences and destroying a series of forts and stockades along the Saigon river, Rigault de Genouilly captured Saigon. The allies were not strong enough to hold the enormous Citadel of Saigon, and on 8 March 1859 blew it up and set fire to its rice magazines. In April Rigault de Genouilly returned to Da Nang with the bulk of his forces to reinforce Thoyon's hard-pressed garrison. On 8 May 1859 he personally led a French attack on the Vietnamese siege lines at Da Nang. The attack achieved limited sucess, but the French were unable to break the siege.
In November 1859 Rigault de Genouilly, whose actions in Cochinchina had been severely criticised in France, was replaced by Admiral François Page, who was instructed to obtain a treaty protecting the Catholic faith in Vietnam but not to seek any territorial gains.
Rigault de Genouilly turned down the offer of command of one of the French fleets during the Franco-Prussian War and resigned as navy minister on the fall of the Second Empire after the battle of Sedan. One of his last acts as navy minister was to order naval personnel and gunboats to take part in the Siege of Paris. After his resignation he retired to Spain to live out his last years. He died in Barcelona in 1873.