This time round the opposition CUF (Civic United Front) is confident it will clinch power.
BBC: NEWS | Africa | Tense Zanzibar prepares for polls
Reuters news agency reports that the CUF activists responded by throwing stones and lighting fires on the streets.
BBC: NEWS | Africa | Zanzibar president wins elections
At their first rally on Saturday, Professor Lipumba of the CUF-Chadema alliance promised to "wage an endless war against corruption".
BBC: Election fever grips Tanzania
Mr Karume got 53% against 46% for CUF (Civic United Front) candidate Seif Sharif Hamad, said Zanzibar Electoral Commission chairman Masauni Yussuf Massauni.
Mr Karume's ruling CCM (Chama Cha Mapinduzi) has also retained its majority in the legislature, with 30 seats against 19 for the CUF.
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