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