Airlangga's sons divided his empire, and Bali was ruled by Anak Wungsu, who established a flourishing kingdom between the Petanu and Pakerisan Rivers, east of Ubud.

The Javanese Majapahit dynasty "conquered' Bali in 1343, when its military forces by the great hero, Gajah Mada subjugated the Pejeng Dynasty, based in Bedulu, just east of Ubud. According to Majapahit reports, the "vile, long-haired Balinese princes were wiped out, " and more refined models of Javanese culture were adopted. Indeed, a great flowering of Balinese culture took place under the Majapahit rulers, who were chosen from the military leaders of the Javanese incursion. Balinese genealogies, the babad, written at this time, document the Majapahit ancestry of Bali's aristocratic families, who still inhabit the palaces of Ubud.

Facing the "Islamisation" of Java and the subsequent decline of the Majapahit Empire in the 16th Century, many scholars, dancers, craftsmen, intellectuals and priest migrated to Bali, bringing along their skills and sacred texts. Many settled in the small kingdoms in and around ubud, among them Nirartha, the "super-priest" who is regarded as the progenitor of all of Bali's pedanda Siwa high priests and their prominent Brahmana families. The seat of the Majapahit overlord of Bali was moved from Samprangan near Gianyar, to Gelgel, and Bali entered cultural " Golden Age" under the Gelgel kings.