The genetic basis of phenotypic evolution is one of the central questions in evolutionary biology. It still remains unresolved how many mutations underlie species' divergence and what is the distribution of their effect sizes. The challenge of genetic analysis between species lies in their reproductive barriers and besides candidate gene studies, few large-scale, high-resolution studies have characterized the genetic basis of species' differences. Here, we performed two genome-wide screens to systematically dissect the genetic architecture of phenotypic divergence between two yeast species, S. cerevisiae and S. uvarum. These two species differ in a number of traits, the most prominent of which is thermal tolerance. In the first screen, we transformed a library of S. cerevisiae genes into S. uvarum and measured their phenotypic effects by competitive growth assays, aiming to identify single genes with independent effects underlying phenotypic divergence. We also carried out a non-complementation screen by crossing the S. cerevisiae deletion collection to S. uvarum, in order to identify genes with effects that depend on a complete complement of the S. cerevisiae genome. Our preliminary results suggest no single genes of large effect underlies the divergence, with the exception of mitochondrial DNA. The results of our interspecific genetic analysis are consistent with a model of multiple changes of small effect and contrast with those of intraspecific genetic analysis.