Remodeling epithelia is a primary driver of morphogenesis. Here, we report a central role of myosin II in regulating several aspects of complex epithelial architecture in the Drosophila eye imaginal disc. The epithelial indentation of the morphogenetic furrow is established from a pattern of myosin II activation defined by the developmental signals Hedgehog and Decapentaplegic. More generally, patterned myosin activation can control diverse three-dimensional epithelial sculpting. We have developed a technique to image eye disc development in real time, and we show that myosin II also regulates higher-order organization of cells in the plane of the epithelium. This includes the clustering of cells into ommatidial units and their subsequent coordinated rotation. This later clustering function of myosin II depends on EGF receptor signaling. Our work implies that regulation of the actomyosin cytoskeleton can control morphogenesis by regulating both individual cell shapes and their complex two-dimensional arrangement within epithelia.