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WASHINGTON — The new mayor of the nation’s capital was hoping to get along fine with Republicans on Capitol Hill.

Instead, they’ve threatened her with prison and she has accused them of acting like bullies in a showdown over legal marijuana that could end up costing District of Columbia residents dearly.

Mayor Muriel Bowser, a Democrat, defied threats from Congress by implementing a voter-approved initiative on Thursday, making the city the only place east of the Mississippi River where people can legally grow and share marijuana in private. But Congress still has the final say over the city’s budget and laws, and the Republicans in charge seem determined to make Bowser pay.

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‘‘We provide half a billion dollars [annually] to the District. One would think they would be much more compliant with the wishes of Congress,’’ Representative Andy Harris, a Maryland Republican and one of the most vocal marijuana opponents, said in an interview Thursday.

Actually, the District received more than $670 million in federal funding last year to support its $11 billion budget. The federal money is earmarked for specific programs — including the city’s court system.

Republicans will ‘‘find some areas where perhaps we have been very generous with the citizens of the District. That will all come with time,’’ Harris warned.

Even top advocates of city autonomy are preparing for tough times on Capitol Hill.

‘‘I do believe it’s likely this is a short-lived victory,’’ said Kimberly Perry, executive director of D.C. Vote. ‘‘Members of the House are going to come after D.C. with a vengeance on appropriations for 2016.’’

Before Bowser announced that she was not backing down, she spoke with the chairman of the House Oversight Committee, Representative Jason Chaffetz, Republican of Utah, and reiterated that her goal is not to defy Congress, but to honor the will of the voters, said her spokesman, Michael Czin.

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‘‘A lot of reasonable people have a different view of this issue,’’ Bowser said Wednesday. ‘‘We believe that we’re acting lawfully.’’

Chaffetz said Congress does not want the District to become ‘‘a haven for smoking pot.’’

But Bowser has emphasized that the change to the marijuana law is limited in scope.

While possession of up to 2 ounces of marijuana or up to three mature plants for use in the home is legal, buying or selling the drug remains illegal, along with smoking in public and possessing marijuana on federal property. The main difference is that city police will no longer be handing out $25 civil fines for possession.

When Republicans are in charge on Capitol Hill, their priorities often clash with leaders of the reliably liberal city, where three out of four registered voters are Democrats.

For example, Congress has prohibited the District from spending any money on abortion, except for a two-year stretch when Democrats controlled the House and Senate as well as the White House. When the abortion restriction was restored in 2011, then-mayor Vincent Gray led a sit-in outside the Capitol and was arrested.

Bowser, then a D.C. Council member, also was arrested in that protest, but she complained that it did not accomplish anything and pledged a more collaborative, less headline-grabbing approach.

What she is finding, though, is that collegiality also depends on who runs the committees.

Gray had a cordial relationship with the previous oversight committee chairman, Representative Darrell Issa. He supported what District leaders call ‘‘budget autonomy,’’ allowing the city to spend its local tax revenue without authorization by Congress.

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But Chaffetz and other Republicans say Bowser could face prison for violating a federal law barring agencies from spending any unappropriated money.