The charges, which Mr Manafort denied, are the first to stem from an inquiry into alleged Russian meddling in the US 2016 election and related to his Ukrainian business dealings.
Richard Gates, one of Mr Manafort’s business partners, was also charged.
A third adviser, George Papadopoulos, has already pleaded guilty to lying to the FBI during the investigation, prosecutors said.
House Speaker Paul Ryan, a leading Republican, said the charges would not “de-rail” tax plans.
But Peter Cardillo, chief market economist at First Standard Financial, said the situation could concern investors: “The market could be awakening to the fact that the political situation is coming back into focus … that could cap the market from moving higher.”
Some firms appeared impervious to the political concerns.
Shares in Apple, which is due to release quarterly results with investors, finished up 2.2%.
Pharmaceutical giant Merck was among the biggest losers after it reported a setback to one of its most important drugs.
Clothing retailers, including L Brands and Macy’s, were also lower.