AMERICANS WHO hope that incoming President Donald Trump will not upend long-standing U.S. alliances or embrace counterterrorism policies that violate civil liberties and human rights have reason to be disturbed by his first national security appointments. The choices of retired Lt. Gen. Michael T. Flynn as national security adviser and Rep. Mike Pompeo (R-Kan.) as director of the CIA could presage a harsh and counterproductive U.S. approach to the Muslim world, a dangerous turn toward Russia and the reembrace of tactics for handling terrorism suspects that violate international law.

Mr. Flynn, a close adviser to Mr. Trump during his campaign, has considerable experience fighting al-Qaeda and other extremist networks in Iraq and Afghanistan. As head of the Defense Intelligence Agency, he is reported to have correctly warned that the terrorist threat was not diminishing in the years after the killing of Osama bin Laden. More recently, however, Mr. Flynn has attracted attention with his rhetorical assaults on Islam and Muslims. He has described Islam as not a religion but a “political ideology” that hides “behind what we call freedom of religion.” He once tweeted that “Fear of Muslims is RATIONAL.”

Mr. Pompeo, who has an impressive academic, military and business record, is known as one of the more fanatical purveyors of conspiracy theories about the 2011 terrorist attacks in Benghazi, Libya, and Hillary Clinton’s alleged responsibility. He dissented from the Benghazi report prepared by his own Republican colleagues, which found no significant wrongdoing. More disturbingly, he has claimed that the U.S. government’s surveillance powers have been critically weakened by reforms designed to prevent abuses. He has called for the creation of a large database combining phone records with “publicly available financial and lifestyle information.”

Mr. Pompeo also has suggested that foreign terrorism suspects should be held for prolonged periods for interrogation by the military or CIA — a policy that would likely revive the Bush administration’s disastrous misuse of the Guantanamo Bay prison.

Mr. Trump has been vague about his plans for fighting the Islamic State and other extremists, but the appointments of Mr. Flynn and Mr. Pompeo suggest a turn toward policies that could deeply alienate U.S. Muslim allies, including Sunni states whose assistance is critically needed to forge political alternatives to the terrorists in Iraq and Syria. An administration that appears to demonize Islam will be welcomed by the recruiters for the Islamic State and al-Qaeda; so will one that returns to the human rights violations symbolized by Guantanamo.

The damage will be compounded if the new administration allies itself in Syria with Russia, as Mr. Flynn and Mr. Trump have advocated. Not only is Russia committing war crimes in its bombing of hospitals and other civilian targets, but also it is doing so in alliance with Iran and the regime of Bashar al-Assad, which only boosts the Islamic State.

Mr. Trump’s choice of Mr. Flynn also raises questions of temperament and conflict of interest. The general was reportedly not renewed in his DIA post because of bad management; since then he has accepted payment from the Russian propaganda network RT, and his consulting firm has lobbied for a businessman close to Turkey’s autocratic president. His arrival at the White House, and that of Mr. Pompeo at the CIA, could trigger the last thing the incoming president should want: an exodus of the seasoned and capable personnel needed to construct a workable foreign policy.