The limb blastema cell, which is a major source of mesenchymal components in the limb regenerate, serves as a stem cell that possesses an undifferentiated state and multipotency. A remarkable property of the limb blastema cell can be seen in its capability for morphogenesis. Elucidation of the molecular basis for morphological regeneration is essential for success in organ regeneration in humans, and characterization of limb blastema cells will provide many insights into how to create three-dimensional morphology during the regeneration process. In this review, we deal with positional memory, a key trait of the limb blastema cell in regard to morphological regeneration, making reference to classic surgical experiments, comparative descriptions of limb and fin blastemas, and genetic/epigenetic regulation of gene transcription. Urodele amphibians, anuran amphibians, and teleosts are likely to share fundamental mechanisms for morphological regeneration, but there are several differences in the process of regeneration, including the epigenetic conditions. Accumulation of knowledge of the molecular mechanisms and epigenetic modifications of gene activation in morphological regeneration of the model organisms for which an overview is provided in this review will lead to successful stimulation of regenerative capacity in amniotes, which only have a limited capability for morphological regeneration.