In 1873 he became interested in improving the various species of grapes native to the United States and planned to do systematic work in the way of developing new varieties by cross-pollination and hybridization.

Munson made extensive use of American native grape species, and devoted a great deal of his life to collecting and documenting them.

He released hundreds of named cultivars, but his work identifying American native grape (especially those from Texas) is of great significance today for their use in rootstock.

Though breeding for wine quality seems to have occupied a great proportion of his effort, his work on rootstock development had the greatest impact on viticulture.

This work provided European grape growers with phylloxera-resistant rootstocks, allowing them to recover from the devastating epidemic of the late 19th century while still growing the ancient Vitis vinifera cultivars.

In honor of this work, the French government named him Chevalier du Merite Agricole, and Cognac, France, became a sister city to Munson's home of Denison.

Later, Munson was also asked to advise on a Phylloxera-resistance rootstock for California vineyards, and through discussions with Luther Burbank he recommended Vitis rupestris.

[6] The U.S. Secretary of Agriculture eventually decided the cost of printing the monograph with the illustrations would be prohibitive, so it was never published in its intended form.