In 1860 they endorsed Lincoln and in 1964 it was LBJ. From the editors of The Atlantic:
Today, our position is similar to the one in which The Atlantic’s editors found themselves in 1964. We are impressed by many of the qualities of the Democratic Party’s nominee for president, even as we are exasperated by others, but we are mainly concerned with the Republican Party’s nominee, Donald J. Trump, who might be the most ostentatiously unqualified major-party candidate in the 227-year history of the American presidency.
These concerns compel us, for the third time since the magazine’s founding, to endorse a candidate for president. Hillary Rodham Clinton has more than earned, through her service to the country as first lady, as a senator from New York, and as secretary of state, the right to be taken seriously as a White House contender. She has flaws (some legitimately troubling, some exaggerated by her opponents), but she is among the most prepared candidates ever to seek the presidency. We are confident that she understands the role of the United States in the world; we have no doubt that she will apply herself assiduously to the problems confronting this country; and she has demonstrated an aptitude for analysis and hard work.
Donald Trump, on the other hand, has no record of public service and no qualifications for public office. His affect is that of an infomercial huckster; he traffics in conspiracy theories and racist invective; he is appallingly sexist; he is erratic, secretive, and xenophobic; he expresses admiration for authoritarian rulers, and evinces authoritarian tendencies himself. He is easily goaded, a poor quality for someone seeking control of America’s nuclear arsenal. He is an enemy of fact-based discourse; he is ignorant of, and indifferent to, the Constitution; he appears not to read.
The full piece is quite interesting as endorsements go.