Ciona intestinalis is a well‐characterized invertebrate model system presenting many advantages to understanding evolutionarily conserved regulatory mechanisms in chordates. Interestingly, the Ciona myocardium is reported to regenerate throughout the life cycle, making Ciona a good candidate for studying heart formation and myocardial repair mechanisms. In order to evaluate the cardiac regenerative response to injury, Ciona hearts were ligated and fixed for TEM or immunohistochemical analysis following 24 or 48 hour recovery periods. Ultrastructure analysis via TEM showed increased sarcomeric disorganization; changes in the sarcolemma; increased intracellular space; increased thickness of an extracellular matrix in the heart lumen, and increased mitochondrial area as time progressed. Modified Movat's Pentachrome staining identified distinct layers of extracellular matrix in the Ciona heart. Specifically, a low collagen contribution as well as punctuate muscle‐specific bodies within the pericardial layer. The luminal extracellular matrix was identified as having a mucin composition. The changes observed in the Ciona myocardium are similar to those observed in zebrafish; however, there are distinct differences in the cellular composition and matrix organization in Ciona. The changes seen in the Ciona intestinalis heart provide an injury model in which further molecular studies could be performed in order to elucidate the regulatory mechanisms of cardiac repair and regeneration in higher order organisms.