Prime Minister Modi paid his respects at the pagoda on the last day of his three-day visit to this Buddhist-majority country.
He also planted a Bodhi tree sapling at the pagoda complex, signifying common cultural heritage, External Affairs Ministry spokesperson Raveesh Kumar said.
"Delighted to visit Myanmar's cultural landmark, the Shwedagon Pagoda," Prime Minister Modi tweeted.
The 2,500-year-old Shwedagon Pagoda enshrines strands of Buddha's hair and other holy relics.
Located west of the Royal Lake in Yangon, Shwedagon Pagoda is considered to be the most sacred and impressive Buddhist site for the Myanmarese people. From a humble beginning of 8.2 metres, the Shwedagon Pagoda today stands close to 110 meters.
Prime Minister Narendra Modi later paid his respects at the Martyrs' Mausoleum and performed 'puja' at the Kalibari Temple.
"Performed Puja at Yangon's Kalibari Temple. Feeling extremely blessed," PM Modi tweeted along with a picture of himself at the temple.
He also visited Bogyoke Aung San Museum with Myanmar's State Counsellor Aung San Suu Kyi Aung San Suu Kyi.
"I thank Daw Aung San Suu Kyi for the special gesture of showing me around the Bogyoke Aung San Museum. Paid tributes to General Aung San," PM Modi said.
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