President
Grover Cleveland nominated Thompson as US Minister Resident to the Republic of
Haiti on May 9, 1885. Thompson was also appointed ''chargé d'affaires'' to the Republic of
Santo Domingo. His nomination was supported by senators
Noah Porter and
Abram Hewitt.
Southern Democratic senators were outraged by Cleveland's nomination of an African American to these posts. Thompson received a Senate confirmation on January 13, 1886, after he had already arrived in
Port-au-Prince. The copy of his credentials was mailed on July 20, 1886. As minister resident, Thompson was called upon, and claimed that he had represented 60,000,000 Americans at Santo Domingo for six years. One of his first assignments was to investigate a homicide allegedly committed by Van Blokklen, an American who was imprisoned as a suspect by the Haitian government. He had to report on the matter to the Department of State. On May 26, 1888, disturbances broke out in Haiti over the presidential elections. The two opposing candidates were exiled on June 6. Haitian politicians applied to the US consulate for asylum five days later. On July 2, military commanders changed. Arson broke out at Port-au-Prince on July 8. The following day, the government asked for United States support by a war vessel. On July 16, discontent about Haitian President
Lysius Salomon resulted in widespread street protests. Salomon abdicated one month and two days later.
Anarchy followed after the abdication. General Seïde Thélémaque led a march at Port-au-Prince on August 25. A provisional government was established by September 5 with the American officers of the
U.S.S. Galena. Fighting broke out again on October 16, and General Thélémaque died in action. Haitian pirates hijacked an American vessel, the
S. S. Haytian Republic. They took it to Port-au-Prince.
Thomas F. Bayard and Thompson sent two warships to force its release, which the Americans achieved. Thompson was widely praised for the negotiations. The following day, General
François Denys Légitime was declared chief of the executive power of Haiti. The French minister was charged with attempted bribery on the next day. In the late 19th century, ships coming from
Caribbean ports sometimes carried passengers with cholera or other infectious diseases such as yellow fever. As the medical community had little understanding of how the diseases were spread, and sanitation was poor in most cities,
cholera and
yellow fever swept through American sea and river ports in more than one epidemic in this period. The US minister was supposed to ensure that ships departing for the United States had no outstanding health issues. Thompson issued such a bill of health against Captain
Francis Munroe Ramsay and his steamship, . The ship was
quarantined for a period in the port of Port-au-Prince before she sailed to New York City. On November 15, 1889, Thompson certified that the
Boston was free of the
plague or
cholera. On November 24, the French minister and the British consul-general announced they had failed to effect a reconciliation of major parties in the north of Haiti to Légitime. Insurgents declared on December 14 that the ports were closed from commerce by decree of the Assembly. Légitime abdicated on August 23, 1889, after an eleven-month rule. It was reported that Thompson spent a contingent expense of $333.02 on travel in 1889 and $130.46 in 1890. Meanwhile, Thompson's deduct repayments amounted to $15. ==Later life==