In Bhutan, clapping is done to ward off evil spirits and not as a welcome gesture.
The gathering, which included Bhutanese Prime Minister Tshering Tobgay and members of the National Assembly and the National Council, however, cheered to applaud Modi.
The joint sessions are held in the chamber of the National Assembly (lower house), attended by members from the National Council (upper house).
Machines were at hand to translate his speech in which he shared his thoughts on India-Bhutan relations.
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At the joint session, the ministers of the Bhutan government were seen wearing an orange robe over their traditional dress, the MPs, 47 from the National Assembly and 25 from the National Council -- were wearing blue robes.
Modi also shared his sentiments at the effusive reception he received not only from the Bhutan government but also the local people.
"Touched by the welcome song sung by primary school students during the luncheon hosted by His Majesty the King of Bhutan," he said in a tweet which also shared its lines, which wished him and Indo-Bhutanese ties success.