Apart from Arya, his son Sanjeev Arya and former party legislator from Yamunotri Kedar Singh Rawat, also joined BJP.
Arya, a Congress veteran, lashed out at party leadership, saying it no longer represented the core values of the party and expressed his faith in Prime Minister Narendra Modi and Shah's leadership.
He, along with was joined with other senior BJP leaders from the state during his meeting with Shah.
Meanwhile, in Dehradun, Uttarakhand BJP hailed Arya's joining of party, saying it was a big jolt to the Congress ahead of state Assembly elections slated next month.
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"It is a big jolt to the Congress. It also vindicates our stand that the party in power was heading for a second vertical split after the first it experienced in March last year when nine party heavyweights deserted it," state BJP spokesman Munna Singh Chauhan told PTI.
"It has now become clear that the Congress in Uttarakhand is a sinking boat which no one wants to ride," he said.
"Arya wields tremendous clout not only in Bajpur, the seat he represented in the state assembly but also in Nainital from where he won several times in erstwhile undivided Uttar Pradesh," he said.
Arya takes the number of sitting Congress MLAs joining BJP after the political crisis in Uttarakhand last year to 11, 10 rebels joining the party earlier who have already been disqualified from the state assembly under the anti-defection law.