The museum established to collect, preserve and exhibit the antiquities retrieved from the excavations, is housed in a spacious structure simulating a Buddhist Vihara on plan. It is located amidst the remains of a medieval fortification, in the northern part of the island spanning about 2.5 km east-west and 1 km north-south. The museum presents precious artifacts of all cultural periods through which the valley and the region have passed. The objects displayed in five galleries include carved lime stone slabs, sculptures, inscriptions and other antiquities all assignable to 3rd-4th century AD constitute a majority of the exhibits.

The key gallery is known for the master pieces of Ikshvaku art and architecture in the form of all pervading serene Buddha, well sculptured ayaka-slabs, the cross beams of ayaka-platforms capturing in all finesse the episodes of the life of the enlightened one punctuated with joyous mithunas and elegant tree nymphs, etc. A separate section with show-cases all along the wall highlights the development of human civilization in the region from Stone Age to the Megalithic period through excavated artifacts and adequate illustrations. Representative minor antiquities like terracotta and stucco figurines, seals and coins form part of the display.

Two galleries located in a large hall, exhibit the decorated drum slabs, dome slabs, cornice beams and other architectural units of a stupa, a few Brahmanical sculptures besides a variety of earthen ware of the Ikshavaku and subsequent periods. The carved architectural units which once decorated the various stupas, capture the life of the Master from his birth to Mahaparinirvana passing through the events of great departure, meditation, enlightenment and preaching. The popular miracles he performed during his life time and the stories of the previous births known as Jatakas like Sasa-jataka, Champeya-jataka, Sibi-jataka, Mandhathu-jataka, etc. also form subjects of carvings. Attractive Brahmanical sculptures displayed here include Kartikeya and his consort Devasena, a Sivalinga, a unique representation of Sati and a few figures of Vidyadharas.

Exquisitely carved mandapa pillars capturing joyous moods of children at play, war scenes and other secular themes, medallions showing elephants in majestic postures and an example of a drawing (hastalekha) on a slab are also exhibited. The ceramic repertoire from excavations form another aspect of display. Fashioned out of fine riverine clay and kaolin, these utilitarian household articles are wheel thrown, polished, designed, inscribed and speak of the technical and artistic excellence of the potters. Third gallery houses models of the submerged valley along with models of secular and religious edifices. On the floor of the hall is the model of the valley with its topographical environs locating over 120 excavated sites. In the wall show-cases all around, are models of important excavated sites and remains. These include Neolithic and Megalithic burials; stupas showing a variety of plan including the Mahastupa; viharas such as the Mahisasaka, Bahusrutiya and Kumaranandi-vihara; Brahmanical temples dedicated to Sarvadeva, Kartikeya, Pushpabhadrasvamin, Ashtabhujasvamin etc. and secular edifices like the amphitheatre (stadium), Bathing Ghat, etc.

One of the galleries displays select specimens of the epigraphs, decorated architectural members and medieval sculptures. The inscriptions are written on pillars forming part of the structural complexes, sculptures, pedestals, memorial pillars and detached slabs. Mostly, the script is ornate Brahmi of 3rd-4th century AD. Majority of them are in Prakrit language and some are composed in Sanskrit. Among the exhibits the inscriptions of Vijaya Satakarni, the memorial pillar depicting king Vasishthiputra Chamtamula, ayaka pillar of Chamta Sri, the Buddhapada inscription and a Sanskrit inscription on a pillar invoking god Pushpabhadrasvamin are noteworthy. A Telugu inscription issued by king Purushottama of Orissa is also on display. The medieval sculptures on display include ornate Yoga-Narasimha, Mahishmardini, Durga, Siva and a Jaina Tirthankara seated in Yoga-posture, ranging in date from 14th-17th century AD.
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