Promoted to commander on 23 January 1806, Seymour became commanding officer of the third-rate HMS "Northumberland", flagship of the West Indies Squadron, in January 1806 and fought under Admiral Sir John Duckworth at the Battle of San Domingo where he was wounded off the southern coast of the French-occupied Spanish colony San Domingo in the Caribbean Sea in February 1806. He went on to be commanding officer of the sloop HMS "Kingfisher" and took part in the blockade of Rochefort. He became commanding officer of the sloop HMS "Aurora" in the Mediterranean Squadron in June 1806 and, having been promoted to captain on 29 July 1806, he was given command of the fifth-rate HMS "Pallas" in February 1808. In HMS "Pallas" he fought under Admiral Lord Gambier at the Battle of the Basque Roads in April 1809. In the summer of 1809 he was called as a witness at the Court-martial of James, Lord Gambier which assessed whether Gambier had failed to support Captain Lord Cochrane at the battle. Gambier was controversially cleared of all charges. He went on to be commanding officer of the fifth-rate HMS "Manilla" in September 1809.