The Seoul central district court's decision to issue a warrant to arrest Lee Jae-yong, 48, a vice chairman at Samsung Electronics and the only son of Samsung chair Lee Kun-hee, makes him the first leader in Samsung's history to be arrested on criminal charges.
The court is also considering whether to issue an arrest warrant for Park Sang-jin, a president at Samsung Electronics and head of the Korea Equestrian Federation, who oversaw the company's external relations, including Samsung's contacts with Choi's company in Germany.
Lee, groomed since his youth to succeed his father in leading the electronics giant with $177 billion in revenue a year, became Samsung's de facto leader after his father fell ill in 2014.
The scandal centres on Choi Soon-sil, who is accused of using her close ties with Park to force local firms to "donate" almost $70m to non-profit foundations which Choi allegedly used for personal gain.
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With the scandal engulfing the group for months, Samsung has not conducted its annual personnel reshuffle and failed to lay out its business targets for this year. Along with bribery, Lee has also been accused of embezzlement and perjury.
"For three weeks, we secured additional evidence that we can be sure about, and after careful deliberation have requested (an arrest warrant) for the second time", spokesman Lee Kyu-chul told reporters without elaborating.
Park has been stripped of her powers while the Constitutional Court decides whether to uphold her impeachment.
Lee's role in the scandal is that he paid bribes to Choi and Park's foundations so that a merger, between Cheil Industries, the holding company for the Lee family, and Samsung's construction company Samsung C&T would be allowed to go through without objection.
On Wednesday, Samsung Group repeated an earlier denial on its official Twitter account: "Samsung has absolutely never bribed the president seeking something in return or sought illicit favours".
His arrest is likely to send shock waves through the group, which is a major part of the South Korean economy.
The merger was opposed by many minority shareholders, who said the deal would hurt them while unfairly benefiting Lee and other members of Samsung's founding family. After his latest conviction in 2008, he was pardoned a year later by the president, who said he would help South Korea's bid to host the 2018 Winter Olympics. The anti-trust regulator was raided earlier this month by prosecutors.