On 22 July 1785 the Baudin brothers bought the "Caroline", a ship of 200 tons, built by the Thébaudière brothers. He was to take the last Acadians to Louisiana. He was a few months behind his brother Alexandre who was captain of the "Saint Remy", built by Jean Peltier Dudoyer. In La Nouvelle Orléans local merchants contracted him to take a cargo of wood, salted meat, cod and flour to Isle de France (now Mauritius), which he did in "Josephine" (also called "Pepita"), departing New Orleans on 14 July 1786 and arriving at Isle de France on 27 March 1787. In the course of the voyage, "Josephine" had called at Cap‑Français in Haiti to make a contract to transport slaves there from Madagascar; while in Haiti he also encountered the Austrian botanist Franz Josef Maerter, who apparently informed him that another Austrian botanist, Franz Boos, was at the Cape of Good Hope awaiting a ship to take him to Mauritius. "Josephine" called at the Cape and took Boos on board. At Mauritius, Boos chartered Baudin to transport him and the collection of plant specimens he had gathered there and at the Cape back to Europe, which Baudin did, "Josephine" arriving at Trieste on 18 June 1788. The Imperial government in Vienna was contemplating organizing another natural-history expedition, to which Boos would be appointed, in which two ships would be sent to the Malabar and Coromandel coasts of India, the Persian Gulf, Bengal, Ceylon, Sumatra, Java, Borneo, Cochin China, Tongking, Japan and China. Baudin had been given reason to hope that he would be given command of the ships of this expedition. Later in 1788 Baudin sailed on a commercial voyage from Trieste to Canton in "Jardinière". He apparently arrived at Canton from Mauritius under the flag of the United States of America, probably to avoid the possibility of having his ship seized by the Chinese for payment of the debts owed them by the Imperial Asiatic Company of Trieste. From there, he sent "Jardinière" under her second captain on a fur-trading venture to the north-west coast of America, but the ship foundered off Asuncion Island in the Northern Marianas Islands in late 1789. Baudin made his way to Mauritius, where he purchased a replacement ship, "Jardinière II", but this vessel was wrecked in a cyclone that struck Port Louis on 15 December 1789.