Houghton was appointed the U.S.
consul in
Santa Fe in 1845. He was serving in that capacity when Santa Fe was occupied by the
United States Army in August 1846, shortly after the start of the Mexican–American War. The
military governor, General
Stephen W. Kearney, quickly formed a civilian
provisional government, and on September 22, 1846, appointed Houghton as Chief Justice of the Supreme Court alongside two associate justices,
Charles H. Beaubien and
Antonio Jose Otero. Like both of his colleagues, Houghton had no legal training, though he read law as a hobby and continued to study it while serving on the bench. As a consequence of Houghton's ignorance of the law, the court's record-keeping was inadequate and irregular, and he also issued no rules of practice to guide attorneys in his court. In the two terms he would ultimately serve on the bench, Houghton apparently filed only one written opinion. Most of the bar of New Mexico at the time, however, was even more ignorant of basic legal principles than Houghton. Even apart from those limitations, the court's functioning was frequently impaired by the military's interference with its orders. In 1847, Houghton presided over several trials for treason resulting from the
Taos Revolt, an insurrection against the American occupation that culminated in the assassination of Governor
Charles Bent. Houghton's dramatic sentencing of conspirator Antonio Maria Trujillo to death by hanging has been frequently noted by historians: It is not certain, however, whether the sentence was ever carried out. Houghton was strongly opposed to slavery and believed its introduction to New Mexico would have a detrimental effect on its people and industries. These views made Houghton extremely unpopular with members of Congress from southern states. In New Mexico's first bid for statehood, Houghton led a faction of anti-slavery delegates in the 1850
constitutional convention. Commanding the majority, Houghton wrote much of the constitution himself, which contained a declaration against slavery and a total rejection of land claims by Texas to portions of New Mexico. Houghton's main political rival in the statehood issue,
Richard Hanson Weightman, viciously attacked Houghton in public speeches and filed charges with the military governor asking for Houghton's removal. Houghton responded by challenging Weightman to a
duel. The duel proceeded and ended anticlimactically. Weightman fired first but missed Houghton. Houghton, being partially deaf, did not hear the command to fire. Before Houghton could take his shot, the seconds intervened and forced Weightman to make an apology of sorts. Their political dispute was largely rendered moot when the bid for statehood was ended by the
Compromise of 1850, which instead organized
New Mexico Territory, and provided that the issue of slavery would be decided by popular vote. ==Between judicial appointments: private practice, political rivalries, and wartime prosecutions==