Dhoni informed the board that he would be available for selection for the upcoming series against England, but wouldn't be continuing in the skipper's role.
"Mahendra Singh Dhoni has informed the BCCI, that he wishes to step down as the captain of the Indian Cricket Team from the One Day Internationals and the T20 Internationals formats of the game," the board said in a statement.
"He will be available for the selection for the One Day and T20I series against England and the same has been conveyed to the Senior Selection Committee," the statement said.
Dhoni captained India in 199 One-day Internationals, winning 110 and losing 74, with four ties and 11 no-results. He has a winning percentage of 59.57. He also led India in 72 T20 Internationals, winning 41 and losing 28, with one tie and two no-results.
Commenting on the development, BCCI Chief Executive Officer (CEO) Rahul Johri said: "On behalf of every Indian cricket fan and the BCCI, I would like to thank M.S. Dhoni for his outstanding contribution as the captain of the Indian team across all formats."
"Under his leadership, Indian team has touched new heights and his achievements will remain etched forever in the annals of Indian cricket," he added.
Dhoni, 35, had earlier suddenly quit Test captaincy during the Australia tour in 2014 in Melbourne.
Most matches as ODI captain— Mohandas Menon (@mohanstatsman) January 4, 2017
230 - Ricky Ponting
218 - Stephen Fleming
199 - MS Dhoni
MS Dhoni as captain...— Mohandas Menon (@mohanstatsman) January 4, 2017
60 in Tests (6th most!)
199 in ODIs (3rd most!)
72 in T20Is (most!)
331 in all internationals (most!)
Dhoni has been India's most successful captain. Under his leadership India have won the ICC T20 World Cup in 2007, the ICC ODI World Cup in 2011, ICC Champions Trophy in 2013 and also reached the top of the Test rankings in 2009.
Test skipper Virat Kohli is the front-runner to replace the Ranchi wicketkeeper-batsman at the helm in all three formats of the game.
(With inputs from agencies)