Marked declines in seagrass meadows are increasingly being reported from coasts around Korea and many regions of the world. The transplantation of seagrasses has been attempted to mitigate and control their degradation from a range of anthropogenic factors. In this study, Zostera marina shoots, which were collected from a donor bed in Koje Bay, were transplanted in Jindong Bay in December 2004. In 2008, a comparative investigation of shoot morphology, growth, and reproduction strategy of Z. marina was carried out between the donor and transplant sites to assess their adaptation success. Shoot height, individual shoot weight, and leaf productivity at the transplant site were significantly greater than those at the donor site. However, below-/aboveground tissue ratio was significantly lower at the transplant site compared to the donor site. Z. marina survival was maintained through vegetative reproduction, while peak season for lateral shoot recruitment was late winter for both donor and transplant site populations. However, vegetative reproduction mainly occurred during late winter and spring at the transplant site, whereas lateral shoots were evident across all seasons except late spring in the donor site. More pronounced seasonal variations were found at the transplant site compared to the donor site. These results indicate that Z. marina populations at the two sites possess distinct phenotypic variations induced by different environmental conditions, and Z. marina transplants have adapted well to the new transplant environment.