Two little-known Fairfax County Republicans are locked in a bitter race for the General Assembly in Northern Virginia's only primary this spring.

The winner of Tuesday's GOP primary in the 39th House district will go on to challenge Democratic Del. Vivian E. Watts, a tough campaigner who helped reshape the state's highway funding formula during her four years in the legislature.

Both Republican and Democratic party officials say they are surprised that two relative political newcomers are eager to challenge Watts. Even GOP leaders say privately that whoever emerges as the nominee will face an uphill fight in the fall elections. Polls in the district will be open from 6 a.m. to 7 p.m., and any registered voter in the district can participate in the primary.

The Republican candidates are Robert E. Murphy, a 52-year-old merchant from Springfield, and Richard N. Vannoy, a 50-year-old Annandale resident who is associate pastor and business manager of Calvary Road Baptist Church and School in Alexandria.

Vannoy, making his first bid for an elective office, has the support of Republican leaders and has outspent Murphy 3-to-1 in the 29,000-voter district in central Fairfax's Annandale area.

The primary is Murphy's second legislative race. In 1983 the former carnival promoter and water bed salesman came in third in a field of three Republicans running for the party's nomination for a state Senate seat. The race was won by former Fairfax City mayor John W. Russell, who also won the general election.

Both candidates in Tuesday's primary are self-described conservatives whose stands on the issues are similar. In the waning days of the campaign, however, each man has suggested that the other is misrepresenting his background.

The chief thrust of Murphy's campaign is to call attention to the fact that Vannoy -- "the Rev. Vannoy," he calls him -- is a clergyman. Murphy charges that Vannoy, a federal worker for 27 years before he went to work at Calvary Baptist in 1981, has tried to play down his involvement with the church.

"He's in politics because of his activities in the church," said Murphy. "His followers are his congregation. My complaint is that he's trying to hide it, trying to pretend that he is not a clergyman."

Vannoy, whose literature mentions that he is business manager of the church but omits his title of associate pastor, denies the charge. "I think he wants to raise the flames of controversy by saying that a churchman should not be involved in politics," said Vannoy, who described himself as a fundamentalist Christian.

Vannoy suggested that Murphy's resume, in which he describes himself as a legislative aide to Del. Gwendalyn F. Cody (R-Fairfax), is not entirely accurate, a charge that Cody tends to support.

She said in an interview that Murphy "spent a week in my office opening mail" during the 1985 session "strictly as a volunteer." She added: "I have my own paid staff."

Told of Murphy's description of his role as a "legislative aide," she snapped: "Don't pick on Bob Murphy. People are loose with some of the things they say."

Murphy, informed of Cody's remarks, exploded: "Oh, my God! Thanks, Gwen."

He insisted that he had not misrepresented his experience, but he said that he had worked as a full-time volunteer for Cody for less than two weeks and had spent most of the time researching Watts' legislative record.

"I wore a badge as a legislative aide for Gwen Cody. I went to breakfasts and receptions as a legislative aide for Gwen Cody. I did everything that a legislative aide does, almost everything that a legislator does, almost everything that Gwen did."

Vannoy said he expects to spend about $10,000 -- including $1,000 of his own funds -- on the primary. Murphy said his spending will come to about $3,000, nearly two-thirds of it from his pocket.