Ben Curtis/Associated Press

A displaced girl carrying water to a United Nations compound in South Sudan. Violence there has uprooted 180,000 people.

JUBA, South Sudan — Few moments conjure as much fear in South Sudan as the massacre of Bor.

Long before South Sudan became a nation, while it was still in the throes of one of Africa's longest civil wars, fighters tied to a leader named Riek Machar stormed through the city of Bor in 1991, killing 2,000 fellow southerners in an attack that would lay bare the deep divisions in this impoverished land.

Since then, the people of South Sudan have had periods of peace, compromise and even shared jubilation at the birth of their nation in 2011. Mr. Machar himself became vice president, apologizing for the massacre.

But there was never a real and lasting reconciliation between the factions threatening to pull this new nation apart, and on Tuesday fighters allied with Mr. Machar charged into Bor once again.

"This was a fire waiting to be ignited," said John Prendergast of the Enough Project, a nonprofit antigenocide organization. "It was just when and not if."

When leaders from around the world pressed South Sudan into existence — seeing its creation as the best way to end decades of war with its neighbor to the north, Sudan — they were well aware that the bitter internal rivalries in the south had never been fully resolved.

To help this fledgling nation's chances, international donors like the United Nations and the United States have pumped in billions of dollars of aid, hoping to create a viable country from one of the poorest places on earth. But what has long been missing, analysts say, is any reliable structure for settling conflicts in a way that would keep the new nation from spinning into a civil war of its own.

"If those issues weren't resolved beforehand, when there was still leverage to keep people at the table, then you were really sowing the seeds for the deterioration of any agreement that was going to be reached," said Charles Stith, an American ambassador to Tanzania during the Clinton administration.

The fighting now tearing at the seams of this nation broke out in a military barracks here in Juba, the capital, on Dec. 15. President Salva Kiir accused Mr. Machar of staging a coup attempt. Mr. Machar denied it but fled to the bush, demanding that Mr. Kiir resign. Fighting between forces loyal to each side quickly spread to at least 20 cities, displacing 180,000 people and killing at least 1,000, probably more, many of them civilians.

But the makings of a crisis existed well before then, in the tenuous marriage of convenience that placed the hopes of this country in the hands of political rivals who often shared long and tortured pasts.

"We didn't suggest who should be No. 1, 2 or 3 in the government; that was their own" choice, said a senior American official, speaking on the condition of anonymity about the negotiations years before independence. "They accepted Riek Machar back into the government."

Instead of governing through strong institutions, many power brokers and generals in this nation still essentially command their own forces, their loyalties to the government often determined by their cut of national oil revenues.

"It is an extortion racket with bargaining ongoing on a regular basis, with either violence or the threat of violence" as a form of negotiation, said Alex de Waal, executive director of the World Peace Foundation at the Fletcher School at Tufts University.

When things break down, the situation quickly plunges into violence. Rebel forces attacked Bor on Tuesday, engaging in fierce fighting with government troops over the city, a strategic location seen as a gateway to Juba. Col. Philip Aguer, a South Sudanese military spokesman, said the fighting was "very intense," while a spokesman for the United Nations said the rebels had captured an airstrip and a major crossroads leading to the capital.

Jacob Achiek Jok, 29, fled Bor on Tuesday morning when the fighters were about to enter town. Many other terrified residents tried to flee as well, he said, either by road or across the White Nile. Some did not make it.

"Many people drowned," Mr. Jok said. "They are normal citizens, not soldiers."