Although unified as a single nation at independence, the south and the north were, from an institutional perspective, two separate countries. Italy and Britain had left the two with separate administrative, legal, and education systems in which affairs were conducted according to different procedures and in different languages. Police, taxes, and the exchange rates of their respective currencies also differed. Their educated elites had divergent interests, and economic contacts between the two regions were virtually nonexistent. In 1960 the UN created the Consultative Commission for Integration, an international board headed by UN official Paolo Contini, to guide the gradual merger of the new country's legal systems and institutions and to reconcile the differences between them. (In 1964 the Consultative Commission for Legislation succeeded this body. Composed of Somalis, it took up its predecessor's work under the chairmanship of Mariano.) But many southerners believed that, because of experience gained under the Italian trusteeship, theirs was the better prepared of the two regions for self-government. Northern political, administrative, and commercial elites were reluctant to recognize that they now had to deal with Mogadishu.

At independence, the northern region had two functioning political parties: the SNL, representing the Isaaq clan-family that constituted a numerical majority there; and the USP, supported largely by the Dir and the Daarood. In a unified Somalia, however, the Isaaq were a small minority, whereas the northern Daarood joined members of their clan-family from the south in the SYL. The Dir, having few kinsmen in the south, were pulled on the one hand by traditional ties to the Hawiye and on the other hand by common regional sympathies to the Isaaq. The southern opposition party, the GSL, pro-Arab and militantly panSomali , attracted the support of the SNL and the USP against the SYL, which had adopted a moderate stand before independence.

Northern misgivings about being too tightly harnessed to the south were demonstrated by the voting pattern in the June 1961 referendum on the constitution, which was in effect Somalia's first national election. Although the draft was overwhelmingly approved in the south, it was supported by less than 50 percent of the northern electorate.

Dissatisfaction at the distribution of power among the clanfamilies and between the two regions boiled over in December 1961, when a group of British-trained junior army officers in the north rebelled in reaction to the posting of higher ranking southern officers (who had been trained by the Italians for police duties) to command their units. The ringleaders urged a separation of north and south. Northern noncommissioned officers arrested the rebels, but discontent in the north persisted.

In early 1962, GSL leader Husseen, seeking in part to exploit northern dissatisfaction, attempted to form an amalgamated party, known as the Somali Democratic Union (SDU). It enrolled northern elements, some of which were displeased with the northern SNL representatives in the coalition government. Husseen's attempt failed. In May 1962, however, Igaal and another northern SNL minister resigned from the cabinet and took many SNL followers with them into a new party, the Somali National Congress (SNC), which won widespread northern support. The new party also gained support in the south when it was joined by an SYL faction composed predominantly of Hawiye. This move gave the country three truly national political parties and further served to blur north-south differences.