A South Korean court on Monday acquitted Lee Jae-yong, Samsung’s top executive, on charges of stock price manipulation and accounting fraud, the latest twist in the billionaire’s legal troubles tied to a merger that helped him secure control of the nation’s largest company.

A Seoul district court judge said that there was not enough evidence to prove the prosecutors’ charges against Mr. Lee and 13 other current and former Samsung officials, including the accusation that the primary intent of the merger was to strengthen Mr. Lee’s power over the conglomerate, against the business interests of each Samsung affiliate that merged.

Prosecutors had sought a prison sentence of five years and a fine of 500 million won against Mr. Lee, 55. He has denied any wrongdoing. Prosecutors have the option to appeal the decision to a higher court. Neither Samsung Electronics nor the prosecutors’ office immediately commented after the verdict.

Mr. Lee’s lawyers said in a statement that the decision “clearly confirmed the legality” of the merger and the accounting of its affiliates.

Samsung is the largest and most successful of the South Korean conglomerates known as chaebol. The group’s electronics arm, Samsung Electronics, alone accounts for about one-sixth of the country’s exports. Mr. Lee, also known as Jay Y. Lee, is South Korea’s wealthiest individual according to Bloomberg News, which estimated his net worth at about $9 billion.

Some South Koreans speak proudly of the chaebol for having helped transform the country from a war-ravaged agrarian economy into a global export powerhouse. But others have increasingly scrutinized whether they stifle smaller businesses or make corrupt deals with government officials without facing enough repercussions.