This persecution was originated by the mad Egyptian Caliph Hakim, a Mahometan Caius Caligula, who believed that he was the incarnation of the divine power, and the vicegerent of God on earth. Hakim persecuted all who dared doubt his divinity—Mahometans, Jews, and Christians, without distinction. At first he decreed that if the Jews of his dominion did not become converts to the Shiitic Islam, they would have to wear round their necks the picture of a calf in commemoration of the golden calf of their ancestors in the wilderness. In addition, they were to be distinguished from the believers by their external appearance, as ordained by Omar. Those who transgressed were to be punished by exile, and by the loss of all their possessions (1008). A similar regulation was enacted against the Christians. When Hakim heard that the Jews evaded his decree by wearing a golden image of a calf, he added a further clause, viz., that they should wear in addition a block of wood six pounds in weight, and have little bells attached to their garments that they might be known at a distance as unbelievers (1010). He afterwards ordered the churches and synagogues to be destroyed, and drove both Jews and Christians out of his kingdom (1014). The Fatimide dominions at that time were very extensive. They embraced Egypt, northern Africa, Palestine and Syria, and since Hakim had adherents also in the Caliphate of Bagdad, there were but few places of refuge open to the Jews. Many, therefore, outwardly conformed to Islam, while waiting for better times to come. The persecution lasted till the Mahometans themselves grew tired of the half-witted Caliph, and assassinated him (1020).

Northern Africa, too, which had enjoyed a brief efflorescence under Isaac Israeli, Dunash ben Tamim, and the alien R. Chushiel, produced its last set of great men in the latter part of the eleventh century, and then sank into oblivion. Its two great authorities were Chananel, the son of Chushiel, the immigrant, and Nissim bar Jacob Ibn-Shahin (1015–1055). They lived in the same place, and are usually named together, but they do not appear to have been on friendly terms with each other. On the contrary, there appears to have been the same rivalry between them as there had been between Chanoch and Ibn-Abitur, Nissim, like the latter, being a native, and Chananel, like the former, the son of an alien. We are not even certain which of the two was the official rabbi of Kairuan; both of them, however, presided over the school. Chananel, in addition, had a large business; whilst Nissim was so poor that he had to be supported by the Jewish minister in Granada. They, however, showed remarkable similarity in their ideas; they pursued the same studies, and wrote works on the same subjects, but Chananel made use of the Hebrew language, and Nissim of Arabic.

A new element in the study of the Talmud, which established it on a firmer basis than that on which the Geonim had been able to place it, was added by the labors of these two men. The Jerusalem Talmud, although more ancient than the Babylonian, had suffered considerably by the fate to which books as well as men are exposed. Whilst the Babylonian Talmud was known and studied in the East to the boundaries of Khorasan and India, and in the West to the end of the ancient world, its companion remained for a long time unknown outside of its birthplace. The former had commentators, who explained and expounded it thoroughly; the latter was for a long time neglected. In consequence of the connection of northern Africa with Palestine, brought about through its conquest by the Fatimide Caliphs, the Jewish teachers of the two lands came into contact with each other, and the Talmud of the Holy Land (as it was called) became known in Kairuan. The two great Talmudists, Chananel and Nissim, were the first in Talmudic circles to busy themselves with it. In their Talmudical writings, which consisted partly of commentaries, explanations of separate words and the subject-matter, and partly of practical decisions, they gave prominence to the Jerusalem Talmud. Both wrote commentaries to the Pentateuch, in which they followed the path marked out by Saadiah for rational exposition of difficult passages in the Pentateuch.

They were both in constant communication with Babylonia on the one hand and with Spain on the other, and formed, so to speak, the link between the two lands. They lived to see the utter extinction of the Gaonate, but after their death the school of Kairuan sank into complete insignificance. One of its pupils, who afterwards became famous as a rabbinical authority, owed his fame solely to his emigration to Spain.

The institutions, too, and the traditions of Babylonian-Persian Judaism showed manifest signs of decay at this time. They possessed, it is true, two men of extraordinary ability, viz. Haï and Samuel ben Chofni, but these were not in a position to stay its dissolution, and could only throw a dim light upon the dying Gaonate.

Haï (or Haya, born 969, died 1038), who had in his eighteenth year been raised to the highest office next to the Gaon, at the age of thirty years succeeded his father Sherira in the Gaonate of Pumbeditha. At his installation the high honor was accorded him of having his name mentioned when a portion from the Prophets was publicly read, and he was compared to King Solomon. Foreign communities, as well as the Babylonians, showed him the highest respect. His character was noble, and he was a man of independent thought. He was versed in all branches of science as they were then taught, and displayed great literary activity. Haï reminds one of Saadiah, whom he took as his model, and whom he defended from attacks, but he was essentially a Talmudist, whereas Saadiah was a religious philosopher. Like him Haï was a thorough Arabic scholar, and made use of that language in many of his letters, and in numerous scientific treatises. Like the Gaon of Fayum he was free from that narrow-minded exclusiveness which permits men to see the truth only in their own religion, and causes them to look upon everything outside as untrue. He was on friendly terms with the head of the Eastern Christians of Bagdad, and on one occasion, when in his exegetical lectures he chanced upon a difficult passage, he did not hesitate to consult the Patriarch (Mar-Elia I.).

In his explanation of rare and archaic words in the Bible, Haï boldly sought assistance from the Koran and the old traditions of the Mahometans in order to confirm their meaning. He was an unprejudiced sage, who loved the light and avoided darkness. He often had disputations with Mahometan theologians about the relation between Judaism and Islam, and is said often to have silenced them by his eloquence. His main study, however, was the Talmud. In this he resembled his father Sherira, but his study was productive of better results. He wrote a terse commentary, in which he explained the words in the most difficult portions of the Mishna and the Talmud.

Haï treated of the civil law of the Talmud, of contracts, loans, boundaries and oaths, with systematic precision. He did this as no one before him had done, and he therefore became the model and authority for later generations. He did not enter upon the field of metaphysics, but although he was not a philosopher, he had sound opinions on mysticism. Surrounded with a halo of religion, a mystic belief often appears reasonable to those of weak reasoning powers, but Haï perceived its deceptive character.

The belief in miracles has, in every country, at all times, and in all creeds, befogged the intellect of unthinking men, and robbed them of the ability to form a rational view of divine wisdom and of life. This belief was fostered by the Jews in many ways, and took as firm a hold on them, as it had on the Christian and the Mahometan world. It was especially prevalent in Palestine and Italy. Its devotees believed that any one who is truly pious can perform at will miracles as great and surprising as those of the prophets of old. They thought, however, that for this purpose it is necessary to pronounce certain magical formulæ, consisting of various combinations of the letters in the name of God. Haï's true religious insight prompted him to write indignantly against this belief, which, despite the fact that his father was not free from it, he considered a desecration of religion. A pupil of Jacob ben Nissim of Kairuan once asked Haï what he thought of the magical power of the names of God, which, many boasted, they could use. Haï answered briefly and sensibly:—"If any one by the mere use of formulæ could perform miracles, and thereby alter the course of nature, wherein lay the distinction of the prophets?" God gave the prophets the power of temporarily altering the laws of nature that they might prove themselves His true messengers. Now, if pious persons could do the same, and if there happened to be many of them, miracles would become daily occurrences, and the motion of the sun from west to east would appear no more extraordinary than its common motion in the opposite direction—in short, miracles would cease to be miracles. "It is wrong," said Haï, "to make use of the name of God for such purposes," and he warned the people against this practice, in which there is much doubt and little truth; and a man must be indeed foolish who believes everything.

Haï was universally acknowledged as an authority, and through his influence the school of Pumbeditha somewhat recovered its prestige. The great scholars Nissim and Chananel of Kairuan, the community of Fez, the vizir Samuel Nagid, Gershom of Mayence, the authority of the German Jews, and the other authorities of the communities of three parts of the world, submitted questions to him, and honored him as the chief representative of Judaism. He was called "the father of Israel." The Exilarchate had been practically extinct since the death of the grandson of David ben Zaccaï, and Haï stood at the head of Judaism. No fitter man could have been found to represent it. Unlike the former Geonim of Pumbeditha, who all looked askance at the sister academy, unlike his father, who felt a keen delight when Sora was without a chief, Haï did his best to give it a leader in the person of Samuel ben Chofni, who filled his office during Haï's Gaonate. Samuel was his father-in-law, and his equal in learning and character. He wrote several systematic works on the ritual, and a commentary on the Pentateuch, in which he set forth the same philosophical views about the unity of God as the followers of the Mutazilist school. His commentary on the Pentateuch, indeed, is not very much praised. It was, like the Karaite commentaries, diffuse, and contained discussions on irrelevant questions. But although his exegetical works mark no distinct progress, yet they show the important fact that the Geonim followed the scientific lines laid down by Saadiah. Samuel ben Chofni's interpretations of the Bible are all rationalistic. He always endeavors to explain the miraculous events narrated in the Bible as if they were natural. He explained the story of the witch of Endor, and of Balaam, as dreams. Like Saadiah, he attacked Karaism, the occasion being a keen controversy which broke out at that time between the Karaites and the Rabbanites. Samuel ben Chofni died four years before his son-in-law Haï (1034), and thus ended the line of the Geonim of Sora.