It is well known that Asa Gray's 1859 essay on the floristic connections between Japan and the United States were among the earliest applications of Charles Darwin's theory to be published before Origin of Species. Commonly known as the “Asa Gray disjunction thesis,” Gray's diagnosis of that previously inexplicable pattern not only established his reputation as a philosophical naturalist and incited debate with Louis R. Agassiz, but also left rich issues for botanists to investigate. This paper examines the making of Gray's 1859 essay and its relation to Gray's intellectual development. The first section focuses on how Gray in the 1830s and 1850s accumulated and arranged those cases suggestive of the floristic relationship between North America and East Asia. The second section details the ways in which Gray in the late 1850s integrated those thoughts—suggested to him by Darwin, George Bentham, Joseph D. Hooker, and James D. Dana—in order to explain the cases he had amassed during the past decades. This paper concludes that though it is clear that Gray deliberately intended to deploy Darwin's theory against Agassiz's, his 1859 essay as a whole should not be regarded as or reduced to a mere application of Darwin's theory to botany. Gray did apply Darwin's theory, but applied it in a way Darwin unexpected.