Dhoni has been named as wicketkeeper in the squads for three one-dayers and three Twenty20 Internationals against England beginning on Jan. 15.
The 35-year-old wicketkeeper-batsman relinquished the limited-overs captaincy on Wednesday after nine trophy-laden years, which included two World Cups and a Champions Trophy.
Having taken over the test captaincy from Dhoni in late 2014 and led the team to top the top of the ICC rankings, the 28-year-old Kohli was a natural choice to skipper the limited-overs squads.
"Virat was on Skype with us...and we chose the best possible squad (for the England series)," chief selector MSK Prasad told reporters.
Kohli took to social media to join the outpouring of tributes to Dhoni's captaincy.
"Thanks for always being the leader a youngster wants to have around him. You'll always be my captain @msdhoni Bhai (brother)," Kohli tweeted.
India's limited-overs stalwart Yuvraj Singh returned to both the one-day and Twenty20 squads after his impressive form in domestic cricket.
Uncapped wicketkeeper-batsman Rishabh Pant was named in the Twenty20 squad which also includes 37-year-old fast bowler Ashish Nehra.
India ODI squad: Virat Kohli (captain), Mahendra Singh Dhoni (wicketkeeper), Lokesh Rahul, Shikhar Dhawan, Manish Pandey, Kedar Jadhav, Yuvraj Singh, Ajinkya Rahane, Hardik Pandya, Ravichandran Ashwin, Ravindra Jadeja, Amit Mishra, Jaspreet Bumrah, Bhuvneshwar Kumar, Umesh Yadav.
India Twenty20 squad: Virat Kohli (captain), Mahendra Singh Dhoni (wicketkeeper), Mandeep Singh, Lokesh Rahul, Yuvraj Singh, Suresh Raina, Rishabh Pant, Hardik Pandya, Ravichandran Ashwin, Ravindra Jadeja, Yuzvendra Chahal, Manish Pandey, Jaspreet Bumrah, Bhuvneshwar Kumar, Ashish Nehra.
(Reporting by Amlan Chakraborty in New Delhi; editing by Ed Osmond)
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