Meanwhile, back on Zanzibar, a power struggle was developing between the Omani rulers. Sultan Thuwaini of Oman planned to overthrow Sultan Majid of Zanzibar, as his promised tribute had not been paid. In February 1859 Thuwaini sailed southwards but was intercepted by a British cruiser at the eastern tip of Arabia. The British government wanted to keep control of the sea route to India, and did not want a civil war to develop in this area. Captain Hamerton, the British consul, had died, but Thuwaini was persuaded to submit his claims to the arbitration of Lord Canning, the Governor-General of India. Thuwaini agreed and returned to Muscat.

But Majid was in danger from another member of the family. His brother Barghash was still plotting to overthrow him and proclaim himself Sultan of Zanzibar. Majid learnt of the plot but Barghash escaped to the Marseilles plantation. He was finally captured and exiled to India for two years. (For more details see The escape to Marseilles box above.)

In April 1861 Lord Canning declared that Oman and Zanzibar should be completely separate states. The annual tribute from Zanzibar to Oman was reinstated and in March 1862 Britain and France signed an Anglo-French declaration which recognised Majid as Sultan of Zanzibar and his territories as an independent sovereignty.

Although the Mwinyi Mkuu still lived in the palace at Dunga, his power was now negligible. Hassan II was succeeded by Mohammed, who died in 1865, aged 80. He was succeeded by his son, Ahmed, who died of smallpox in March 1873, leaving no male heir. The line of the Mwinyi Mkuu of Zanzibar had come to an end, and its passing was hardly noticed.

In 1866, in Oman, Thuwaini was murdered in his sleep by his son, Salim, who succeeded him. Majid discontinued the payment of the tribute on the grounds that Salim was a usurper, and Oman withdrew into isolation. (This isolation lasted for over a hundred years, until the accession of Sultan Qaboos bin Said in 1970.)