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In 642 AD the Arabian general Amr Ibn El-As conquered Egypt during the first rapid phase of the expansion of Islam. He was a member of the Prophet Mohammad's own tribe, Quraysh. He became Muslim in about 630 AD.

By the time the Arabs reached Alexandria, the Arab forces, inspired by the new religion of Islam and led by Amr Ibn El-As, had already captured the strategic fort of Babylon near modern Cairo. They advanced towards the capital, Alexandria, and camped near present Nouzha Gardens. Amr, who was a political rather than a commander, negotiated a treaty with the Roman viceroy, the Patriarch Cyrus. The treaty was signed on November 8th 641AD, and Amr and his soldiers entered a city which contains 4000 palaces, 4000 baths and 400 theatres.

Amr was appointed as ruler of Egypt, and he had to make a critical decision. He knew the Arab civilization was of the land, not of the water. Omar Ibn El-Khatab, the Muslim Caliph, had bitter memories about thousands of soldiers drowning in Persia when a bridge fell on the Euphrates. "Establish your capital wherever you wish, but let be no water between you and me", said Omar. This meant that Alexandria could not serve as the Capital as long as the Nile river existed. The Arabs moved east of the Nile, where they established another city, Al-Fostat, the nucleus of modern Cairo.

For the next thousand years, the glamour of Alexandria declined. The Arabs greatly admired the city, and the most descriptive accounts of the Pharos Lighthouse and the monuments come from Arab records. But they were more interested in Al-Fostat, their new capital. They were horsemen, not sailors, and the Mediterranean meant little for them.

When the lantern of the Lighthouse fell in the 8th century, and when the building collapsed during the 956 and 1323 earthquakes, they had no plans for repair. In 1498, the fort of QuaietBay was eventually constructed on the foundation of the Pharos. Among the few landmarks constructed during the Arab period are the Shrine of Abdul-Dardaa, a Muslim scholar and one of the companions of the prophet Muhammad; and the mosque of Al-Mursi Abul-Abbas, an Andalusian-style mosque built by the Murcian immigrant.

Alexandria was further struck by the discovery of the new route around Africa to the Far East. The port would not regain its power until he inauguration of the Suez Canal in the mid 19th century. The population of the city shrank, and was centered in the vicinity of the newly accreted land around the heptastadion. The area, formerly known as the Turkish town, later became the city center (El-Mansheya).

Towards the end of the Mamelouk rule (late 18th century), corruption reached its peak. Egyptians were burdened by heavy taxes, and were scientifically and economically lagging behind other nations. Europe had started witnessing global political changes with the French revolution and the emergence of Napoleon as a military and political leader. And, indeed, the Frenchman gave Egypt a wake-up call on July 1st, 1798.