Abstract: Our efforts to associate phenotypic variation with genetic variation increasingly recognize that the function of genes is dependent on the environmental and genomic contexts in which they occur. Consequently, we seek an understanding of the developmental and physiological systems from which phenotypes emerge. Similarly, our pursuit of genes and evolutionary processes that contribute to reproductive isolation and speciation will require that these be embedded within the relevant environmental and genomic contexts. In this talk I will present relevant data from two lines of research that use the genome composition of hybrids to draw inferences about reproductive isolation and the speciation process. In natural hybrid zones we have found evidence for remarkably complex genetics of isolation in different taxa, with variability across the genome and points of contact between species. In diploid hybrid species we have estimated the time scale over which the species became isolated from ancestral taxa and have developed methods to detect genomic regions that were shaped by selection and contributed to isolation in the nascent species. The research employs analyses that integrate over the many processes that shape the composition of hybrid genomes. Whereas these approaches lack the experimental control of more typical mapping experiments, they have the advantage of embedding the genetics within the natural context within which species' boundaries arise and are tested by hybridization.