The groups have spread terror in northeastern and central Nigeria and are blamed for thousands of deaths as they battle to set up an Islamic state.
"These designations are an important and appropriate step, but only one tool in what must be a comprehensive approach by the Nigerian government to counter these groups," the State Department said yesterday.
The shadowy groups' insurgency has claimed many lives since 2009 and triggered concern over its potential to spread across the porous borders in the region.
White House advisor Lisa Monaco said the decision cuts "these terrorist organizations" off from US financial institutions and allows any assets held in the United States to be frozen.
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Nigeria welcomed the decision and expressed the hope that the United States would step up intelligence cooperation.
"We salute the US government for its effort in partnering with Nigeria to rout out terrorism," Justice Minister Mohammed Adoke told AFP in Abuja.
"We hope that with this development that the Boko Haram menace will soon become a thing of the past."
State Department spokeswoman Jen Psaki explained it had taken time to blacklist the groups because "Boko Haram is a decentralized and factionalized organization with a loose command and control structure."
The United States, she added, had "worked over the years ... To deepen our understanding of the organization."
While Washington believes Boko Haram and Ansaru remain "primarily" Nigerian organizations, "both these groups have links to AQIM," she added, referring to Al-Qaeda's north and west African affiliate.