John Wilmerding, a scholar in the field of America's art history, has been chosen to become second-in-command at the National Gallery of Art.

As assistant director, under J. Carter Brown, Wilmerding will be in charge of the museum's works of art and its curatorial staff. He will succeed Charles Parkhurst, 69, who will retire from the gallery on Jan. 31.

Wilmerding, 44, taught 12 years at Dartmouth College, where he chaired the art department and the humanities division, before he joined the gallery in 1977 as senior curator and curator of American art. Though his new job will involve broad administrative duties, Wilmerding, who is known for both his scholarship and diplomatic skills, said yesterday, "I hope to keep my hand in scholarship and teaching."

Art is in his genes. He is the great grandson of Louisine Havemeyer, who, in the 1890s, at the instigation of her friend Mary Cassatt, began buying modern paintings by Courbet and Manet, Degas and Ce'zanne. She bought Old Masters too--Goyas and El Grecos and half-a-dozen Rembrandts. She, her son and daughter eventually presented 1,972 pictures to the Metropolitan Museum of Art.

Wilmerding is one of a small group of Harvard-trained Americanists who, in recent years, have taken high positions in American museums. A number of his Harvard colleagues--among them Earl A. (Rusty) Powell, now director of the Los Angeles County Museum of Art, and Theodore E. Stebbins Jr., curator of American art at the Boston Museum of Fine Arts--contributed essays to the catalogue for "American Light," the Luminist exhibit he organized in 1980.

At present he is working on two shows. One will be a study of the boxing pictures of George Bellows; the second will be called "Important Information Inside: The Art of John F. Peto and the Idea of Still Life Painting in 19th Century America."

The gallery is now raising funds with which to purchase works of art, and Wilmerding expects to be involved in all new acquisitions. He has written 14 books. Born in Boston, he graduated from St. Paul's in 1956, and then went to Harvard, where he wrote his thesis on the history of American marine painting.