ALBANY — One would be hard-pressed to find two political parties that agree on less than the liberal Working Families Party and the Conservative Party of New York, which occupy opposite ends of New York’s political spectrum.

But they do agree on one thing: Democratic leaders in New York are out to eliminate them.

In separate, but parallel, lawsuits filed on Monday, the two parties have accused Gov. Andrew M. Cuomo and other top Democratic officials of effectively conspiring to try to get rid of them via a leave-no-evidence manner familiar to Albany: through the creation of a special commission.

One of the commission’s primary tasks will be to examine the state’s practice of fusion voting, the electoral oddity whereby candidates in New York are able to run and collect votes on multiple party lines, sometimes representing wildly divergent political philosophies.

Most states do not allow such crossover, but supporters of fusion voting in New York say that it allows for more political ideas to percolate, as major party candidates seek their party endorsements.

The calculus and stakes for such small parties are plain: Any group that gets 50,000 votes in an election for governor is guaranteed a ballot line for the next four years. Any group that does not is banished from the ballot, effectively ending any influence it might hold, and — in some cases — the third party itself.

The legal action also comes with a subplot, pitting the State Democratic Party — which is effectively led by Mr. Cuomo, now in his third term — against the Working Families Party, a progressive-backed group that supported Mr. Cuomo’s opponent, Cynthia Nixon, in last year’s Democratic primary. (In an example of fusion voting, the party gave Mr. Cuomo its line in the general election, where he collected more than 100,000 votes.)

On Monday, Bill Lipton, the state director of W.F.P., said that the commission was aimed squarely at ending fusion voting, and the party itself.

“Cuomo always tries to destroy what he can’t control,” Mr. Lipton said. “Fortunately, the State Constitution protects this important right.”

Mr. Lipton also accused the governor of protecting “Republican control in Albany,” during his first two terms by allowing a group of rogue Democrats, the Independent Democratic Conference, to work with Republicans to control the State Senate. The W.F.P. backed a series of successful primary challenges against I.D.C. members last year.

Hours later, Mr. Cuomo’s camp shot back.

“Lipton joining forces with the pro-Trump, anti-woman and anti-L.G.B.T.Q. Conservative Party proves once and for all that he has no ideology,” said Rich Azzopardi, a senior adviser to Mr. Cuomo. “It’s only about personal power, hypocrisy be damned.”

The W.F.P. lawsuit also shows fault lines in both the Democratic Party in a deep blue state and the all-Democratic Legislature in Albany: the plaintiffs, for example, include a handful of Democratic lawmakers, who have filed a suit against the Assembly speaker, Carl E. Heastie, a Bronx Democrat, and the Senate leader, Andrea Stewart-Cousins, a Democrat from Westchester County.

One of those plaintiffs is Assemblyman Walter T. Mosley, a Democrat from Brooklyn, who said that the fusion voting system was “a valuable part of our election system, which gives voters more choice and brings light to more issues.”

“The creation of a commission aimed at rolling back fusion voting rights was a mistake,” said Mr. Mosley, who said he voted against the budget deal in large part because of the special commission. “And I don’t believe it will hold up in court.”

Many Democrats accept the W.F.P.’s endorsement, but also run on the lines of other parties, too. When the governor was elected to a third term in November, for instance, he ran on four lines, including the Independence Party, a third party which often backs Republicans.

Richard Brodsky, a former state assemblyman and a lawyer for the W.F.P. and other plaintiffs, said that the practice of fusion voting had been a constitutional right for more than a century, and had been repeatedly upheld by the courts.

“We do not have to the prove the wisdom or importance of fusion voting,” said Mr. Brodsky, a Democrat who represented Westchester County. “The other side has to prove why they, by the path of law, should be allowed to interfere with a fundamental constitutional right.”

William F. Savino, a lawyer for the Conservative Party, echoed that, saying that he fully expected the commission to recommend that fusion voting be ended, despite what he described as public support.

“If you ask most New Yorkers should their political party have the right to endorse the candidate their party feels is most qualified, they would say yes,” said Mr. Savino. “And if you ask them if their party should still have the right to endorse that candidate, even if another party had endorsed the candidate before, they would still say yes.”

In their lawsuits, the plaintiffs argue that the Legislature effectively overstepped its authority in creating the commission, in a deal struck during this year’s budget process. Under that agreement, the nine-person commission would issue a report in December whose recommendations would be binding unless modified by the Legislature within 20 days.

Mr. Brodsky said that the legal effort to protect fusion voting would not address the commission’s work on public financing of campaigns, which the W.F.P. supports and is not subject to the suit.

Mr. Cuomo has not taken a public position on the issue, but in March, the state party passed a resolution calling for an end to the practice, a move that drew the ire of several prominent Democrats, including Representative Alexandria Ocasio-Cortez of Queens and Senator Elizabeth Warren of Massachusetts.

Jay Jacobs, the chair of the state party and a member of the newly formed commission, said on Monday that the commission would be “fair-minded” and would hold hearings and “listen to people.”

“The W.F.P. and the Conservative Party have every right to do what’s in their best interests,” said Mr. Jacobs, who is also a defendant in both suits. “But what I’m going to do is look out for what’s in the best interests of all the voters in the State of New York.”

Jesse McKinley is The Times’s Albany bureau chief. He was previously the San Francisco bureau chief, and a theater columnist and Broadway reporter for the Culture Desk. @jessemckinley

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