But reverberations are also being felt in Moscow.
The Kremlin is now confronted with embarrassing revelations that Flynn and the Russian ambassador to the United States, Sergey Kislyak, did discuss US sanctions last December, despite repeated denials to the contrary.
US officials suggest the conversation -- which took place before Flynn officially joined the US government -- could have been used by the Kremlin to blackmail the close Trump adviser.
When asked by CNN on Tuesday, a Kremlin spokesman said Flynn's resignation is a US domestic matter and not for Russian officials to comment upon.
Other Russian officials have been less circumspect, defending Flynn while suggesting anti-Russian motives lay behind his departure.
"The target is not Flynn," tweeted Aleksey Pushkov,
a senior Russian lawmaker, "but the relationship with Russia."
Konstantin Kosachev, the current chair of the Foreign Affairs Committee of the Russian Federal Council, wrote on Facebook that Flynn's openness to dialogue with Russia was seen as a "thought-crime" in Washington.
"Either Trump has not gained the required independence and subsequently (and unsuccessfully) is being backed into a corner, or Russophobia has already infected the new administration from top to bottom," Kosachev wrote.
The comment casts light on one of the Kremlin's main concerns: that US politics is so poisoned against Russia that Trump -- who has voiced sympathetic views towards Russia -- may opportunistically reverse his pro-Russian stance and adopt more critical policies, if only to ensure the political survival of his administration.
Already, there are possible signs of the Trump administration hardening its stance.
The Trump-appointed US ambassador to the United Nations, Nikki Haley, recently criticized Russia for its role in the conflict in eastern Ukraine, and reiterated that US sanctions would remain in place against Russia until Crimea, annexed by Russia in 2014, is returned to Ukraine.
As a presidential candidate, Trump suggested he would consider recognizing Crimea as part of Russia.
It has also been reported that Trump reacted unfavorably to President Vladimir Putin's suggestion that Russia and the US renew an Obama-era nuclear weapons agreement.
Is this a win for Putin?
On the one hand, the Kremlin had high hopes for the Trump administration, which appeared to share Russia's world view on issues from Islamic extremism to NATO expansion.
Those hopes could be in the process of being dashed.
But chaos in Washington could still play to the Kremlin's advantage, allowing Putin to highlight the instability gripping Trump's America and contrasting it with the relative stability and calm in Putin's Russia.