What is known is that Mr. Botín’s father, also called Emilio, left Spain with part of his wealth in late 1936, after the start of the Spanish Civil War, fearing, like many other Spaniards, what might come.

The elder Mr. Botín spent a few months in London before moving to Basel, Switzerland, and eventually returning to Spain to resume leadership of the bank that he had run since 1933. But while he returned to Spain, the money he salted away in Switzerland did not. The senior Botín died in 1993. Last year, the French government passed on to Spain data that it had obtained from Hervé Falciani, a former employee in HSBC’s Swiss subsidiary, naming almost 600 Spanish holders of secret bank accounts. Among those was one belonging to the estate of Mr. Botín’s father.

In his opening summary, the judge in charge of the case, Fernando Andreu, highlighted “the complexity of the hereditary structures” of trusts, foundations and other companies set up to oversee the account. The closest he came to explaining what was in the account was to say that it also included a 12 percent stake in Bankinter, a midsize bank in which Jaime Botín, Emilio’s brother, is a leading shareholder. That holding, at current stock market value, would be worth about $310 million.

Representatives for Mr. Botín have said that the family has voluntarily paid what it owes and that Mr. Botín expects that the government will agree and close the case. It seems altogether likely that Mr. Botín and his family will be cleared of any wrongdoing, which would come as no surprise to the banking patriarch’s fiercest critics.

“Santander is not only too big to fail but it is also the best corporate brand image that Spain has — so nobody in the government, judiciary or elsewhere is ever going to question seriously what they do,” said Antonio Panea, a lawyer and shareholder gadfly who has fruitlessly sued the institution on a dozen claims.

All of which misses the point, Mr. Botín’s defenders argue.

“I’m convinced that the Botíns are not motivated by money, they are motivated by love of banking,” said Mauro F. Guillén, a management professor at the Wharton School at the University of Pennsylvania and author of a book on Santander’s rise to prominence. “If they were interested in maximizing their own wealth, they would have diversified out of Santander.”

Luis Arenzana, a portfolio manager in Madrid who worked at Santander as an investment banker in the early 1990s, said: “Some of what Santander has done was borderline ‘alegal’ rather than illegal. But then to be investigated occasionally for possible misconduct is the normal state of affairs for any large bank — anybody who succeeds in Spain is always suspected of wrongdoing.”