<p><strong> </strong>Comparison of tissue-specific gene expression profiles between sibling species and their F1 interspecific hybrids are expected to reveal important information about the mechanisms involved in speciation and species divergence. In the present study, the expression of 40 candidate genes were analyzed using qRT-PCR in the testis, ovary and head tissues (both male and female) among the hybrids and their parental species. The expression patterns of these genes were profiled via quantification of misexpression (both over- and under-expression) relative to that of their parents as well as across tissues. We set out to answer several questions as well as test the following hypotheses: (1) Do <em>Drosophila</em> sibling species differ in tissue-specific distribution of gene expression? (2) Do males and females differ in tissue specific distribution of expression? (3) Do reciprocal crosses differ in patterns of gene misexpression suggesting X-effect? (4) Do sex and non-sex genes differ in extent of gene misexpression? The results of this study gave rise to two important findings. First, it was found that while the majority of genes showed head and testis expression in <em>Drosophila melanogaster</em>, more genes showed head and ovary expression in <em>D. sechellia</em>. Second, we observed differences in gene misexpression between reciprocal <em>D. simulans </em>and <em>D. sechellia</em> hybrid females, suggesting the role of maternal effect. Thus, these findings supply a wealth of data regarding tissue-specific expression in both fertile females and sterile male hybrids, the former of which have largely been ignored, as well as advance our understanding of the process of species divergence and speciation. Ultimately, this thesis will provide a contribution to the field of gene regulatory evolution.</p> / Master of Science (MSc)