Abstract: To address intra-group and inter-group communication issues arising from function heterogeneity in heterogeneous sensor networks (HSNs), the applications of public-key cryptosystem, especially identity-based encryption (IBE), is studied, and a key management protocol for HSNs based on multi-domain identity-based encryption (M-IBE) is proposed. In the protocol, one group of HSNs is analogized to one domain in M-IBE from a logical point of view. Before deployment, a trusted third party generates global public parameters for the HSN, selects public and private keys for each group, and extracts private key for each sensor within the group. After deployment, neighbor sensors within the same group set up shared-key through the exchange of sensor identity; neighbor sensors in different groups establish shared-key after getting authorized from cluster heads. The proposed protocol is composed of four parts: key material pre-distribution, shared-key establishment within group, shared-key agreement between two groups, and adding new sensors and removing sensors. The security analysis and performance evaluation show that the protocol has high security, which can resist against high-end sensors and low-end sensors capture attacks. It also has low storage requirements and constant connectivity probability. It can satisfy the demand for higher security application scenarios.