Zanzibar forms a separate state within the United Republic of Tanzania. It is governed by a Revolutionary Council and House of Representatives, whose members are elected or appointed. The president of Zanzibar is also the vice-president of Tanzania.

Zanzibar has seen many changes on the political front since the early 1990s. Along with the rest of Tanzania, Zanzibar ceased to be a one-party state in 1992. For the first time in almost 20 years Chama Cha Mapinduzi (CCM) was faced with several new opposition groups, which quickly coalesced into parties. The Civic United Front (CUF), led by Seif Sherif Hamad from Pemba, became the major opposition party for Zanzibar. Elections were planned for October 1995, as all parties agreed that a gradual transition to a multi-party political system would be beneficial. Salmin Amour remained Zanzibar's president and CCM leader, while on the mainland the CCM chose a new president, Benjamin Mkapa, in July 1995. This followed the resignation of Julius Nyerere, the 'father of the nation' who had ruled since independence, although he remained an important figure behind the scenes.

Elections were duly held in Zanzibar on 22 October 1995, a week before the mainland vote. It was a simple two-horse race between Salmin Amour and Seif Sherif Hamad for president of Zanzibar, and between CCM and CUF candidates in the islands' parliament. There was a very high turnout (over 95% of registered voters) and voting passed peacefully, but the counting took three days for just over 300,000 votes.

Although the ruling party's control of the government structure gave it an in-built advantage, it soon transpired that the CUF was polling strongly. Complaints by the CCM that the election process was flawed were withdrawn when it transpired that Amour had won with 50.2% of the vote, but then the CUF picked up the claim of unfair procedures. International observers agreed that there was evidence of serious irregularities, but the nominally independent Zanzibar Electoral Commission refused to hold a recount or to compare their figures with some of those recorded by the UN. On the mainland, a divided opposition and an even more shambolic election, not to mention the possibility of vote-rigging, meant that the CCM and President Mkapa stayed in power. The CUF brought a high-profile legal case against the CCM on the grounds that the results and the whole election process were not representative of the wishes of the people, but this was bogged down in the courts and finally dismissed in 1998.

In the lead-up to elections in late 2000, Amour rocked the boat by announcing he would stand for a third (and unconstitutional) term as president. The instant response among the people of Zanzibar was a sharp swing in support for the CUF. An equally quick response from CCM high command meant Amour was relieved of his post, and Amani Karume, son of President Karume who had been assassinated in the 1960s, was ushered in as Zanzibar's new CCM leader and presidential candidate.

At a grassroots level, there was still considerable support for the CUF, but the strong Pemba following this party enjoyed meant that ostensibly political differences stood in danger of degenerating into inter-island (or 'tribal') conflicts. This sense of grievance also translated into separatist aspirations; since the end of the 1990s, the desire of many Zanzibaris to be independent of mainland Tanzania has been stronger than it has been for many years. The urge for separation is also partly due to the death in 1999 of Julius Nyerere.

When elections were held in October 2000, President Mpika and the CCM romped home with huge and increased majorities. The people of mainland Tanzania seemed happy (in fact, many seemed indifferent) about the result, and international observers agreed that voting had been free and fair. On Zanzibar, however, it was a different story. In the period leading up to the election, fist-fights erupted on several occasions between CUF and CCM supporters, local party offices were attacked or burned, and CUF demonstrations were broken up by the police and army. On election day, things were so bad in 16 constituencies that the whole process was cancelled, and a re-run vote arranged for 5 November. CUF demonstrations turned into violent protests, especially in Zanzibar Town, to be met with police tear gas, rubber bullets and even live ammunition. In disgust, the CUF pulled out of the election process, leaving the November re-runs to be easily won by CCM candidates. In response, the CUF announced its continued boycott of procedures in the House of Representatives.

In one of his first moves as newly elected president of Zanzibar, Amani Karume called for peace and reconciliation between the two sides, which he backed up by releasing from prison the group of CUF leaders who'd been held on charges of treason since 1998. Hopes for peace were dashed shortly afterwards when a series of bombs exploded in Zanzibar. The trouble simmered on, with more CUF street protests in January 2001. This time the police used even stronger tactics to break things up: in a single day, between 20 and 70 demonstrators were shot, one policeman was killed, and many more were injured. The events were reported in media around the world, the USA and the donor nations of Europe expressed concern, and aid money which had been frozen following the discrepancies of the 1995 election remained firmly out of reach.

In March 2001, at the direct behest of President Mkapa, leaders from the CCM and the CUF tentatively started to discuss their differences, and in October that year, after a long series of negotiations, the two sides signed an accord to end their dispute over the election results. By 2002, the islands had returned to their traditional calm and peaceful atmosphere, and Zanzibar was fully open for business once again.

The most recent elections were held in October 2005. Once again, the CCM and the CUF were vying for power, with rallies held across the island throughout the summer of 2005. Although there seemed to be little in the way of party manifestos, and despite claims by the CUF of vote rigging and other irregularities, this time the election passed off comparatively peacefully. With a 90% turnout of the electorate, the CCM retained control, with the CUF polling 46% of the total votes, and Amani Karume retaining the presidency.