Flores, who became the youngest president in the Americas when he took his oath of office on 1 June 1999, wants to form a broad-based government, which he has dubbed the "New Alliance." He is known to be an independent thinker and may find himself at odds within his own party, particularly with former president Alfredo Cristiani, who has let it be known that he wants to influence the shape of the government.
Flores has to contend with determined opposition from at least one faction within the FMLN. The FMLN had been gaining popular support during the last several years, winning the election in San Salvador's mayoral race and capturing nearly an equal number of legislative seats to those held by ARENA. In the 1999 election, division surfaced between hardline socialists and moderates during the party's nominating process. FMLN candidate, Facundo Guardado, more moderate than some elements within his wing of the party, nonetheless indicated his lack of enthusiasm for working with Flores. His actions will also be closely followed by the Roman Catholic Church, which has been pressing the government to provide more security, better education, and improved health care.
In the March 2000 legislative races, FMLN won 31 seats in the Legislative Assembly and the ARENA won 29.