This paper examines the controversy between two early American geneticists, William E. Castle (1867-1962) and Raymond Pearl (1879-1940). Scientific controversies among US geneticists have attracted relatively little attention because historians have mainly seen early American genetics as dominated by Thomas Morgan’s “Fly Room” at Columbia University. Focusing on Morgan’s fly genetics has led historians to undervalue the importance of the agricultural context in the development of genetics in the United States. However, a majority of early American geneticists worked at agriculture-related institutions, and they argued over theoretical and practical issues relevant to agriculture. The Castle-Pearl controversy offers a revealing example. At the time the controversy unfolded in 1915-1917, both Castle and Pearl were working on agriculture-related genetic experiments at agricultural institutions: Castle at Harvard’s Bussey Institution and Pearl at the Maine Agricultural Experimental Station. While their experiments had the same goals – testing genetic theories and developing practical breeding methods – they reached different conclusions about several critical issues: the validity of the pure-line theory, the efficacy of mass selection in practical breeding, and the role of natural selection in evolution. As they admitted, their diverging views derived from their different interpretations of their own breeding experiments. The central question is: What led Castle and Pearl to interpret their experiments in different ways? To answer this question, I focus on the implications of practical breeders’ knowledge and breeding techniques to the research conducted by Castle and Pearl, in order to draw a more detailed intellectual and institutional map of early American genetics.