Tunicates are marine animals close to vertebrates, and have the ability, unique among chordates, to form large colonies of clonal individuals. Among tunicates, the most frequently studied ascidians represent an ideal model for investigating aspects of epigenetics evidenced during the various phases of the life-cycle. Interestingly, the typical mosaic development of eggs and embryos of ascidians, considered as a classic example of autonomous genetic control of genes for specification of cell lineage, may now be interpreted in the light of cytoplasmic and extracellular influences on the regulation of gene activity. In addition, the capacity of several species to create similar individuals by means of two different developmental pathways - embryogenesis and blastogenesis - and the high regulative power shown by colonies in natural or experimental modifications of the environment, reveal the importance of the epigenetic phenomena (interactions) during the entire life cycle of these animals. Two species are of particular importance as models, the solitary Ciona intestinalis (whose genome has been recently sequenced) and the colonial Botryllus schlosseri. We report here examples of epigenetic phenomena in ascidians, to show that the various stages of the entire development of the phenotype are driven by a dynamic interplay of genome, cellular components and tissues, and their micro- and macro-environments