DnaJ proteins act as molecular chaperones to maintain protein homeostasis under stress. However, their role in seagrass remains largely unidentified. We found that the expression of ZjDjB1, a class II J gene of Zostera japonica, was up-regulated under low-temperature stress. Therefore, we cloned ZjDjB1 from Z. japonica, a typical intertidal seagrass. The role of nuclear and cytoplasmic-targeted DnaJ protein (ZjDjB1) in Z. japonica was studied. Under low-temperature stress, the rates of germination and survival of overexpressed Arabidopsis thaliana were higher than those of the wild-type (WT); the root length was longer; the detached leaves were more tolerant to low temperature, and the chlorophyll content of leaves, relative water content and dry weight of shoot were higher. Overexpressed plants accumulated more osmotic protective substances under low-temperature stress, and the antioxidant enzyme activity of overexpressed plants was higher than that of the WT plants. Under low-temperature stress, overexpressed plants accumulated fewer reactive oxygen species. The root cell viability of overexpressed plants was higher than that of WT under low-temperature stress, and there was minimal membrane damage in the overexpressed plants. Furthermore, the level of expression of CBF1 and CBF target genes, including KIN1 and COR15B, was higher in overexpressed plants than that in the WT plants when subjected to low temperature. These results indicate that ZjDjB1 plays an important role in plant resistance to injury under low-temperature stress.