Other top picks in the first four rounds were goalkeeper Subrata Paul, who was picked by Jamshedpur for Rs 87 lakh and right-back Pritam Kotal, grabbed by Delhi Dynamos for Rs 75 lakh.
"He (Lyngdoh) was our no. 1 pick. He also scores goals and should be valuable," ATK coach Teddy Sheringham told reporters.
Asked what style ATK wanted to play, the coach quipped, "winning style."
Steve Coppel, Jamshedpur FC's head coach, said: "Picking Indian players is a priority and we will try and match the skeleton of the team. A decision on choosing foreign players will be taken soon."
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"We had a terrific and solid players in the pick. Now our job is to cement the team."
Mumbai City FC picked striker Balwant Singh (Rs 65 lakh) in the third round and goalie Arindam Bhattacharya (Rs 64 lakh) in the fourth round. Rino Anto went to Kerala Blasters for Rs 63 lakh.
A total of 24 players were drafted at the end of first four rounds.
ISL's founder chairperson, Nita Ambani, earlier announced that Hero MotoCorp has extended its title sponsorship of the League for another three years, amounting to INR 160 crore.
The 4th edition of the ISL is set to commence on November 17 and a total of 95 matches are to be played in four months, with two new teams increasing the size of the event.
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