Tissue morphogenesis can be broadly defined as the progression by which tissues achieve their functional shapes. It is directed by key developmental processes such as cell type differentiation, modulations to the overall number of cells, the regulation of cell adhesion, and changes in cell morphology. Defects in morphogenesis can lead to impaired tissue function resulting in reduced fitness or death. The study of the cellular mechanisms which facilitate tissue patterning and organization is therefore of paramount importance to the field of developmental biology. The ethical and legal restrictions on human experimentation have led to the use of several model organisms and tissue systems that are used to study tissue morphogenesis. One such system is the Drosophila melanogaster pupal eye. The pupal eye presents an ideal model system, in part because it has a highly stereotyped arrangement of cells that are grouped into a honeycomb lattice. This allows trained researchers to identify subtle changes in cell organization resulting from genetic manipulation. In addition, the eye is post-mitotic allowing for the study of changes in cell behavior independent from any effects of proliferation. In this work we detail a pupal eye dissection protocol for immunohistochemistry, western analysis, and RNA extraction. We utilize the RNA extraction technique to compare transcriptomes of wildtype pupal eyes of different developmental ages in order to better study the transcriptional changes that choreograph pupal eye development. These analyses identified differential expression of genes with established roles during pupal eye morphogenesis encompassing multiple biological processes such as signaling, axon projection, adhesion, and cell survival. In addition, our analyses identified differential expression of loci not previously implicated during pupal eye morphogenesis including components of the Toll pathway, several non-classical cadherins, and components of the muscle sarcomere; raising the possibility these genes function as novel patterning factors. In addition to using transcriptome analyses to identify genes required to choreograph pupal eye development, we utilized transcriptomics as part of a study examining the role of the Hippo signaling pathway during pupal eye morphogenesis. In Chapter IV of this work, we show that Hippo signaling is required to pattern the Drosophila pupal eye. In particular, we focus on the role of the protein Multiple ankyrin repeats single K homology domain (Mask). Our data shows that Mask, the Hippo pathway transcriptional effector Yorkie (Yki), and the Yki negative regulator Warts are required for pattern formation and for maintaining Adherens Junction (AJ) integrity in the pupal eye. Our study also revealed that Mask regulates the expression of established regulators of AJs and the actin cytoskeleton. We chose to focus on the role of two of these loci, FER and Vinc, and demonstrate a requirement for both during pupal eye morphogenesis.