Morphogenesis is a process describing how the shapes of living tissues and bodies are created during development. Living and fossil organisms exhibit enormously diverse tissue architecture and body forms, although the functions of organs are evolutionally conserved. Current knowledge reveals that relatively conserved mechanisms are applied to control development among different species. However, the regulations of morphogenesis are quite diverse in detail. Animals in the ocean display a wide range of diversity of morphology suitable for their seawater environment. Nevertheless, compared with the intensive studies on terrestrial animals, research on marine animal morphogenesis is still insufficient. The increasing genomic data and the recently available gene editing methods, together with the fast development of imaging techniques, quantitative analyses and biophysical models, provide us the opportunities to have a deeper understanding of the principles that drive the diverse morphogenetic processes in marine animals. In this review, we summarize the recent studies of morphogenesis and evolution at molecular, cellular and tissue levels, with a focus on three model marine animals, namely ascidians, sea urchins and sea anemones.