The senator, Roy J. McDonald of Saratoga County, announced his decision Thursday.



“After discussing the issue with family, friends, campaign staff and trusted advisors, I’ve decided that I will not actively campaign in the general election on the Independence Party line,” Mr. McDonald said in a statement.



Mr. McDonald, who was first elected to the Senate in 2008, will still appear on the ballot as the endorsed candidate of the Independence Party. The Republican nominee is Kathleen A. Marchione, the Saratoga County clerk, who defeated Mr. McDonald in the Sept. 13 primary; she will face a Democrat, Robin Andrews, who is the Claverack town supervisor.



Mr. McDonald said he would support Ms. Marchione in the Senate race.



“Moving forward, I will be supporting all Republican candidates – including Kathy Marchione – in the general election, because I believe maintaining the Republican majority in the New York State Senate will continue to positively change state government,” he said. “It is important to recognize the need for checks and balances in our democracy, which can only be assured by a multi-party system.”



Ms. Marchione issued a brief statement thanking Mr. McDonald.



“I congratulate Roy McDonald on a hard-fought race and I appreciate his support,” she said. “He’s a good man who works tirelessly for our community. Roy and I have been friends for more than 20 years. The primary, and everything that came with it, is behind us, and I still count him as a friend.”



Mr. McDonald’s decision increases the likelihood that the Republicans will hold the Senate seat, which would help them retain their narrow majority.



“Roy’s decision was a difficult one, but ultimately it was the right choice for his party and for this Senate district,” the Senate majority leader, Dean G. Skelos, a Long Island Republican, said in a statement. “The last thing he or anyone wanted to do was to turn this upstate seat over to the New York City-dominated Senate Democrats.”



In a three-page statement, Mr. McDonald cited his work for people with disabilities, and for veterans, but did not refer explicitly to the same-sex marriage issue.



“I am very proud of my time in public service,” he said. “Standing up for the communities I represented was always my first priority. I have been a senator for all people.”



Mr. McDonald’s announcement comes one day after Gov. Andrew M. Cuomo, a Democrat, offered to endorse Mr. McDonald in a third-party bid for re-election, and a number of gay-rights groups pledged to provide financial support for such a campaign. But on Thursday, Mr. Cuomo acknowledged at a news conference that a third-party bid by Mr. McDonald would have been “uphill.”



Of the four Republican senators who voted in favor of same-sex marriage last year, at least two will not be returning to Albany in January: Mr. McDonald, and Senator James S. Alesi of Monroe County, who did not seek re-election. The other two, Senator Mark J. Grisanti of Buffalo and Senator Stephen M. Saland of Poughkeepsie, won Republican primaries this month and are seeking re-election in November.



Danny Hakim contributed reporting from Albany.