The desiccation tolerance of the intertidal seagrass Zostera japonica has been demonstrated in a number of studies; however, the factors limiting expansion of intertidal seagrass species into subtidal zones remain controversial. We transplanted Z. japonica shoots from the intermediate intertidal zone into the plots with and without Z. marina shoots in both the lower intertidal and shallow subtidal zones to investigate the factors controlling Z. japonica growth in these zones. Daily photon flux density at the Z. japonica canopy level was attenuated by both water depth and coexisting Z. marina shoots but more strongly by Z. marina shoots than water depth in the transplant plots. The shoot density and biomass of Z. japonica transplants were significantly lower in transplant plots in the subtidal zone than in the lower intertidal zone. Although the photon flux density was significantly lower in transplant plots containing Z. marina shoots, the growth of Z. japonica transplants did not differ significantly between plots with and those without Z. marina shoots. Z. japonica transplants exhibited photoacclimatory responses such as increased shoot height and chlorophyll content under the lower-light conditions, offsetting the reduced light availability so that no significant differences in transplant growth occurred between plots with and those without Z. marina shoots. As the growth of Z. japonica transplants decreased significantly in the subtidal zone, the interactive effects of environmental stresses associated with tidal inundation and reduced light availability may restrict penetration of the intertidal seagrass Z. japonica into the subtidal zone. The persistence of high photosynthetic performance after air exposure and a regular arrangement of the densely overlapped leaves atop wet sediments may be desiccation tolerance mechanisms for Z. japonica in the intertidal zone.