Recent years have witnessed the prosperous development of Graph Self-supervised Learning (GSSL), which enables to pre-train transferable foundation graph encoders. However, the easy-to-plug-in nature of such encoders makes them vulnerable to copyright infringement. To address this issue, we develop a novel watermarking framework to protect graph encoders in GSSL settings. The key idea is to force the encoder to map a set of specially crafted trigger instances into a unique compact cluster in the outputted embedding space during model pre-training. Consequently, when the encoder is stolen and concatenated with any downstream classifiers, the resulting model inherits the `backdoor' of the encoder and predicts the trigger instances to be in a single category with high probability regardless of the ground truth. Experimental results have shown that, the embedded watermark can be transferred to various downstream tasks in black-box settings, including node classification, link prediction and community detection, which forms a reliable watermark verification system for GSSL in reality. This approach also shows satisfactory performance in terms of model fidelity, reliability and robustness.