The African population of the French Territory of the Afars and Issas voted overwhelmingly as expected today to end 115 years of French colonial rule and become Africa's 49th independent nation on June 27.

The overall results of the refendum will not be known officially until Monday, but there was no question her that both the Afars and Issas, who make up the vast majority of the territory's 215,000 people, had voted massively for independence.

Less certain was how much support the single list of 65 candidates for the interim Constituent Assembly commanded in the elections held simultaneously with the referendum. The majority of the candidates are Issas, assuring that the first independent government here will be Issa-dominated and pro-Samali.

Two of the Afar parties called upon their supporters to hand in blank ballots to protest the choice of the candidates but their influence over the Afars is unclear. Several Afar leaders supported the single list, including Ali Aref, the behind-the-scenes strongman of the main opposition group, the National Union for Independence.

In the last referendum on independence in March 1967, 60 percent of the 37,000 inhabitants who participated voted to remain part of France. The referendum was boycotted by the Issas, however, and the French were widely accused by Africa of having interferred in the voting to assure a favorable outcome.

The territory, which will become the Republic of Djibouti on June 27, is France's last colony on the African continent. It was served mainly as a Red Sea and Indian Ocean base for the French armed forces. Aside from the 6,500 military personnel stationed here - including 800 soldiers of the French nationals in the territory. Many of these either have already left or plan to leave.

France went to great lengths to assure that the referendum and elections would be held without serious incident and recognized internationally as legitimate. Observers from the United Nations, the Organization of African Unity and the Arab League were taken by car, plane and helicopter to many of the 102 balloting stations set up throughout this desert territory to witness the voting.

France also closed the 320-mile frontier with Ethiopia and Somalia to prevent the infiltration of outsiders and put its forces here on alert in case of incidents.

The main French concern is to withdraw without leaving a political mess that could encourage either of the new nation's neighbors to invade. Both Somalia and Ethiopia are extremely interested in the fate of this strategically located bit of land on the straits of the Bab el Mandeb, at the entrance to the Red Sea.

Somalia has long aspired to see it integrated into a "Greater Somalialand" of Somali-speaking peoples throughout the region. Ethiopia, with its main railroad running from its capital to the port of Djibouti, regards the territory as its main access to the sea.

In hope of preventing political instability that could touch off a Somalia Ethiopian confrontation, France and the Organization of African Unity arranged a United front comprising both Afars and Issas. It was this Issa-controlled front that was responsible for selecting the 65 candidates, including 30 Afars, for the Constituent Assembly and it has been the only political grouping actively involved in the lethargic election campaign.

The main Afar party, the National Union, urged its supporters to vote "yes" to the question, "Do you desire to see the French Territory of the Afars and Issas independent," but to abstain from supporting the list of assembly candidates.

The Afars' political leadership is so badly fragmented, however, that it was doubted that more than 30 per cent of the Afars would follow this advice. There are even some National Union village leaders among the 65 candidates.

The voting seems to have gone smoothly thoughout the territory, according to scattered reports from foreign correspondents and international observers.

In Dikhil, a hilltop village of 4,500 people 75 miles inland from Djibouti near the Ethiopian border, there was no sign of trouble. Although the village is predominantly Issa, the Afars make up 70 per cent of the 18,000 electors in the district. The two ethnic groups, which have often fought with each other in local and national feuds, voted peacefully side by side at three different voting places in or near the village.