Twelve years in the political wilderness have ended for Mexico’s Institutional Revolutionary Party (PRI) with the victory of Mr. Enrique Peña Nieto in this month’s presidential election.

Even after a recount confirmed Mr. Peña Nieto’s win, the opposition is claiming fraud and continues to challenge the result. The odds of an overturn are practically nonexistent, but that is the least of the new president’s concerns: He inherits a country that faces deep and seemingly intractable challenges.

Mexico’s president can only run for one six-year term. In theory, that ensures that each election is fought among equals, with no incumbent exploiting an institutional advantage.

In practice, the PRI has, by virtue of 71 years in power until getting the boot in 2000 and the deep ties with national constituencies that seven decades of rule created, enjoyed a boost in electioneering. The party and its candidates have deep pockets and large national bureaucracies that get out the vote.

Whatever the cause — and it is contested — Mr. Peña Nieto prevailed in the ballot, winning 38.21 percent of the vote; coming in second was the veteran leftist political leader, Mr. Andres Manuel Lopez Obrador of the Party of Democratic Revolution (PRD), who won 31.59 percent of ballots cast, a difference of more than 3 million votes (and only fractionally different from the results released immediately after the polls were held and closed on July 1).

In a telling verdict on the National Action Party (known by its Spanish initials PAN), which has ruled the country for the last 12 years, candidate Josefina Vazquez Mota came in third, with about a quarter of the vote (25.41 percent). While that should be a humbling assessment of her party’s performance, PAN may have more leverage than it thinks.

Mr. Lopez Obrador has not accepted the results, even after the recount. He did the same after the 2006 presidential vote, which he lost to Mr. Felipe de Jesus Calderon (now the outgoing president) by about half a percentage point. He then called his supporters into the streets and virtually paralyzed Mexico City for months.

There is little chance of his prevailing this time: His margin of defeat is much larger, the electoral rules were written with parties from the left in mind, and the left approved the judges and electoral officials overseeing the ballot. While there appears to be evidence of some vote buying, there is little indication that it was large enough to influence the outcome.

But even if Mr. Peña Nieto’s margin of victory is handsome, governing will be a challenge.

The new president won a plurality of voters, but nearly two-thirds of the electorate voted for other candidates. Nor does his party have a majority in either house of the Mexican Congress; the governors of many states, another source of considerable power in Mexico’s federal system, also either belong to opposition parties or have different priorities from the president. This is where support for PAN may matter.

Although the party has been discredited as largely ineffectual — the economy grew on average a miserable 1.5 percent a year over the last 12 years, and Mr. Calderon’s war on drugs created a level of insecurity for many Mexicans that is unprecedented in the country’s modern history — it may well find common cause with many of Mr. Peña Nieto’s policies.

The new president faces two sets of problems, both stemming from so-called cartels. The first is the extraordinary level of violence unleashed by Mr. Calderon’s attempts to take down the drug cartels. An estimated 60,000 lives have been lost in the six years since that offensive began, at the cost of billions of dollars, human rights abuses and the deployment of tens of thousands of troops across the country. Spillover effects include kidnapping, extortion and a pervasive atmosphere of fear.

As a candidate, Mr. Peña Nieto’s most important promise was to cut crime and violence in half, but he has not proposed a radical change in policy. He has pledged to continue to work closely with the United States to deal with the drug problem.

The second set of cartels are those of business interests that have had a stranglehold on the Mexican economy for generations.

The PRI’s seven decades of rule perpetuated a concordance of political and business interests that Japan knows only too well. Monopolies dominate the economy in sectors ranging from communications to concrete.

Mr. Peña Nieto’s promise to achieve economic growth of 6 percent depends on breaking those vested interests. Historically, however, those groups have been well protected by the PRI. Thus, one of the new president’s biggest challenges will be lining up his party behind him. On its face, that might be difficult.

Mr. Peña Nieto has been groomed for the presidency, with boyish good looks and considerable support from the nation’s media. He is the new face of the party, but the first instinct of the old boys will be to teach him the realities of governing once he takes office.

Still, after 12 years out of power, the party will be reluctant to pick early fights with the new president, especially given his limited support in the legislature. And, again, the prospect of PAN support may strengthen the new president’s hand.

There is little chance, however, of bold reform or big changes in Mexico. Incrementalism will be the hallmark of Mr. Peña Nieto’s administration. Given the situation in Mexico, that may be more than enough.

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