The Vaitulyas, despite their suppression by Voharika-Tissa, began to assert themselves again at the Abhayagiri in the days of Gothabhaya (309-322 AD). When the Dhammarucikas (or the residents of the Abhayagiri) accepted Vaitulyavada, a mahathera called Ussiliya-Tissa himself a leading monks at the Abhayagiri left the place with about three hundred monks and lived at the Dakkhanagiri cut off from the Dhammaruci sect. One of this new group, a mahathera named Sagala, formed a new sect called Sagaliya at the Dakkhinagiri.

Gothabhaya held an enquiry, suppressed the Vaitulyakas, burnt their books, and exiled sixty of their leaders from the Island. Some of the exiled monks left Sri Lanka and stayed at Kavirapattana in south India. These monks in south India became intimately connected with a young monk named Samghamitta, who later became the champion of Mahayanism in Sri Lanka. Samghamitta got an opportunity to succeed in his designs during the reign of Mahasena (334-362AD), that happened to be one of his disciples. Mahasena in Sri Lankan history is the first man who had the courage to stand against the authority of the Mahavihara. Sanghamitta who resided at the Abhayagiri, worked with Mahasena tried in vain to convert the Mahavihara to Mahayanism. For 9 years the Mahavihara was deserted, Mahasena demolished the seven-storeyed Lohapasada and many other buildings of the Mahavihara, and utilized their materials to erect new buildings at the Abhayagiri.

The popularity of the Mahavihara was so great that public opinion turned against the king afterward. Mahasena was, thus, brought to his senses and realized his error in time and agreed to restore the Mahavihara. Though the king had agreed to restore the Mahavihara, but he was still hostile to it. He therefore built the great Jetavana within the boundaries of the Mahavihara ignoring the strong protests of its authorities, and dedicated it to a thera named Tissa of the Dakkhanagiri and a follower of the Sigaliya sect. As a consequence, the Mahavihara was abandoned once again for nine months. Tissa Thera was charged in the assembly of monks with having committed an offence of the gravest kind. Meghavanna-Abhaya, disrobed Tissa even though the king was against such an action. Mahasena's power as secular head of the religion was evidently weakened by his rash acts.

Mahasena's eldest son, Siri-Meghavanna (362-409AD), who succeeded him, apologized to the monks of Mahavihara and made ample amends for the damage done. In the ninth year of his reign arrived the left eye-tooth of the Buddha from Dantapura in Kalinga. It is remarkable that the Mahavihara should have had no part in the worship of the Tooth Relic which became the national palladium of the Sinhalese. Sri Meghavanna also sent an embassy to the Indian king Samudragupta for permission to build a monastery at Bodhagaya monastery. Another Sri Lankan monk, Prakhayakitti erected a dwelling place at Bodhagaya.

The famous Chinese pilgrim Fa-shian came to Sri Lanka during the reign of Buddhadasa (beginning of the fifth century AD) the well-known physician king, who provided extensive facilities for both men and animals. It was during his reign that thera Mahadhammakathi translated the Pali suttas for the first time into Sinhalese. The Abhayagiri was flourishing at that time, most probably after Mahasena's activities. According to Fa-shian, there were 5,000 monks at the Abhayagiri, while there were only 3,000 at the Mahavihara.

During the time of Buddhadasa's son, Upatissa I, a new festival called Gangarohana was inaugurated on the advice of the monks to overcome a famine which occurred early in the fifth century. His brother Mahanama (409-431AD) was favorable to Abhayagiri, while his queen was devoted to the Mahavihara. It was during the time of Mahanama that the commentator Buddhaghosa came to Anuradhapura, and while residing at the Mahavihara, translated the Sinhalese commentaries on the Tipitaka into Pali. In 433AD Sri Lankan nuns introduced the Sangha of nuns into China.

Dhatusena(460-478AD),was originally a monk but gave up his robe, did a lot of work to promote Buddhism as well as the welfare of the country. He was a staunch supporter of the Mahavihara and built 18 great viharas and tanks and offered them to the monks of the Theriya sect. He also renovated the Ambatthala-vihara on the Cetiya-pabbata with the idea of giving it to the Theriyas. But on the entreaty of the Dhammarucikas who were in occupation of the hill since the days of Mahasena, the vihara was granted to their sect. Dhatusena made several statues of the Buddha and the Bodhisatta and built houses for them.

Dhatusena was succeeded by his patricide son Kassapa I (478-496 AD) of Sigiriya fame. At first the monks of the Theriya sect were not favourable to him chiefly through fear of public censure. They refused to accept his offer of the Issarasamanarama that was enlarged and enriched with new endowments by Kassapa. but later on they yielded and allowed it to be offered to the image of the Buddha, thus, accepting it indirectly. Kassapa I built a vihara for the Dhammarucikas as well.

An important event that took place during the reign of the next king Moggallana I (496-513 AD), it was the bringing of the Hair Relic of the Buddha (Kesadhatu) to Sri Lanka. Mogallana also purified the Sasana which was disorganized during the troublesome days of Kassapa I. King Silakala (524-537 AD), who was formerly a monk, decreed the order of non-killing over the Island, maintained hospitals, and carried on the usual religious activities.

The celebrated poet-king Culla-Mogallana or Mogalana II (537-556 AD) had the Tipitaka preached along with the Commentaries. He also made arrangements for the books to be written down. He himself composed a religious poem and seated on the back of his elephant, recited it at the end of a sermon in the city at night. He was so anxious to disseminate learning that it is recorded he lured children with sweetmeats to study the dharma.

A great thera called Jotipala, who came from India, defeated the Vaitulyas in the Island in a public debate during the reign of Aggabhodi I (568-601 AD). After this public defeat there were no more converts to the Vaitulya doctrine. The Abhayagiri and the Jetavana dismissed pride and lived in submission to the Mahavihara. This indicates the importance of the Mahavihara in the sixth century AD. Around this time, there was frequent religious intercourse between India and Sri Lanka and many Sri Lankan monks are said to have made frequent visits to the Buddhist shrines at Bodhagaya.

The next king Aggabodhi II (601-611AD) does not seem to have taken interest in the Mahavihara. He built Veluvana-vihara for the monks of the Sigaliya sect. During his time, the king of Kalinga, on account of some political trouble there, came to Sri Lanka and became a monk under Jotipala thera.

Dalla-Moggallana or Moggalana III (611-617 AD) held a grand recital of the three pitakas and encouraged the spread of religious knowledge by honoring the learned. This gave an impetus to Buddhist literary activity. He too purified the Sasana. King Kassapa II (641-650 AD) repaired the buildings that had been destroyed and performed many religious activities. He also arranged for monks to go about and preach the dharma, and caused a compendium (sangaha) of the Pali texts to be composed. He also had the Abhidhamma recited alone with the Commentaries. This new interest in the Abhidhamma was becoming an outstanding feature of the intellectual class of the period. Shuan-chang records that the Sinhalese monks "were distinguished for their power of abstraction and their wisdom."

During the time of Dathopatissa II (650 -658 -AD) there was again some friction between the king and the Mahavihara. Dathopatissa wanted to build a vihara for the Abhayagiri, but the Mahavihara raised objection on the ground that it was within their boundaries. But the king forcibly carried out his plan. The monks of the Theriya sect were bitter against the king and applied to him the "the Turning Down of the Alms-Bowl (patta-nikkujjana-kamma), which is considered the excommunication of a layman. But the king did nothing against the Mahavihara. These facts clearly signify the important position occupied by the Mahavihara in the seventh century AD.

Aggabodhi IV (658-674 AD) made ample amends for all the injustices done to the monasteries by his kinsmen in the past including the previous king his elder brother. All the three nikayas received his favor. To the three fraternities he gave a thousand villages with large assured revenues. The whole country followed the example king. Even the Tamils, who were high officials in the service of the king, followed him in his religious activities. The queen built a nunnery for nuns and provided all comforts for them. For the first time we have the example from the reign of Aggabodhi IV to the chanting of paritta as a ceremony, which became a regular feature of later Buddhist practices. He also proclaimed the order of non-killing. After this a new spirit of regard for animal life can be noticed that began to influence the minds of the people. Kassapa III (711-724 AD) decreed not only the order of non-killing, but also reared fish in two ponds. Aggabodhi VII (766-772 AD) not only purified the Sasana, but also became the first Sri Lankan king to occupy Polonnaruva as his capital on a permanent basis. Mahinda II (772-792 AD) and Sena I (831-851 AD) are reported to have made provision for fishes, beasts, and birds, while Udaya I or Dappula II (792-797 AD) is said to have given corn to cattle and rice to crows and other birds.

King Udaya II (885-896 AD) was the last king to govern from Anuradhapurra. The great Lohapasada, the nerve center of Buddhist activities in olden days, had now only 32 monks as residents, even after it was repaired. All interests and activities, both political and religious, were fast shifting into the rich, capital of Polonnaruva, now growing rapidly in importance and size.

By about the tenth century, this belief had become so strong that the king of Sri Lanka had not only to be Buddhist but also a Bodhisatta. The Jetavanarama Slab Inscription of Mahinda IV (956-972 AD) declared clearly that a ksatriya becomes a king for the purpose of defending the alms-bowl and the robe of the Buddha. The king as the defender of Buddhism, was so highly respected that even words originally used in reference only to the Buddha and the arahants, came to be applied to the rulers of Sri Lanka. Similarly, Kirti Nissanka Malla (1187-1196 AD) says in his inscriptions that Lanka belonged to Buddhism and that therefore non-Buddhists had no right to the throne of Sri Lanka.

In the 16th century the Portuguese conquered Sri Lanka and savagely persecuted Buddhism as did the Dutch who followed them.

When the British won control at the beginning of the 19th century Buddhism was well into decline, a situation that encouraged the English missionaries that then began to flood the island. But against all expectations the monastic and lay community brought about a major revival from about 1860 onwards, a movement that went hand in hand with growing nationalism.

Although occasional extraneous influences have entered the culture, all those pollutions were repulsed by a firm opposition from both the Sangha and the laity, as was the attempt to introduce into this country a Mahayana Sect of the Japanese clergy as recently as 1990.