In November 2001, the National Party won presidential and parliamentary elections. The PNH gained 61 seats in Congress and the PLH won 55. The PLH candidate Rafael Pineda was defeated by the PNH candidate Ricardo Maduro, who took office in January 2002. Maduro administration emphasized on stopping mara growth, especially Mara 18 and Mara Salvatrucha.
On 27 November 2005 the PLH candidate Manuel Zelaya beat the PNH candidate and current Head of Congress Porfirio "Pepe" Lobo, and became the new President on 27 January 2006.
Jose Manuel Zelaya Rosales of the Liberal Party of Honduras won the 27 November 2005 presidential elections with less than a 4% margin of victory, the smallest margin ever in Honduran electoral history. Zelaya's campaign theme was "citizen power," and he vowed to increase transparency and combat narcotrafficking, while maintaining macroeconomic stability. The Liberal Party won 62 of the 128 congressional seats, just short of an absolute majority.
In 2009 Zelaya caused controversy with his call to have a constitutional referendum in June to decide about convening a Constitutional National Assembly to formulate a new constitution. The constitution explicitly bars changes to some of its clauses, including the term limit, and the move precipitated a Constitutional Crisis. An injunction against holding the referendum was issued by the Honduran Supreme Court. Zelaya rejected the ruling and sacked Romeo Vásquez Velásquez, the head of Honduras's armed forces. Vásquez had refused to help with the referendum because he did not want to violate the law. The sacking was deemed unlawful by the Supreme Court as well as by the Congress and Vásquez was reinstated. The President then further defied the Supreme Court by pressing ahead with the vote, which the Court had deemed "illegal". The military had confiscated the ballots and polls in a military base in Tegucigalpa. On June 27, a day before the election, Zelaya followed by a big group of supporters entered the base and ordered, as Commanding Officer of the Armed Forces, for the ballots and polls to be returned to him. The congress saw this as abuse of power and ordered his capture.
On June 28, 2009, the military removed Zelaya from office and deported him to Costa Rica, a neutral country. Elvin Santos, the vice-president during the start of Zelaya's term, had resigned in order to run for president in the coming elections, and by presidential line of succession the head of Congress, Roberto Micheletti, was appointed president. However, due to the stance taken by the United Nations and the Organization of American States on use of military force to depose a president, most countries in the region and in the world continued to recognize Zelaya as the President of Honduras and denounced the actions as an assault on democracy .
Honduras continued to be ruled Micheletti's administration under strong foreign pressure. On November 29, democratic general elections were held, with former Congressional president and 2005 nominee, Pepe Lobo as victor.