Objective: To develop a protein-based multi-modality imaging probe namely bCD-PLL-Cy5.5 Conjugate-1 and to non-invasively monitor probe labeled endothelial progenitor cells (EPCs) in tumor neovascularization. Methods: Bacterial cytosine deaminase (bCD) protein was modified with poly-L-lysine (PLL) that is labeled with imaging reporters including T1 weighted magnetic resonance imaging (MRI) contrast chelator and near infrared (NIR) fluorophore. EPCs isolated from rabbit peripheral blood were labeled with Conjugate-1 by co-culture. Cell proliferation, cell cycling and cell uptake kinetics were evaluated. 2×106 labeled cells were transplanted into a MDA-MB-231 tumor bearing mice, both magnetic resonance imaging and near-infrared fluorescence imaging were performed at different time point. Results: Conjugate 1 showed low cytotoxicity in EPCs. The normalized cell viability maintained above 90% after incubation for 1-5 days. Flow cytometry studies demonstrated cells were effectively labeled in 24 hours. After cell transplantation, signal enhancement of tumors in T1WI and significant reduction of T1 relaxation time were obtained from MRI. NIR optical imaging also demonstrated the “homing” EPCs in tumor area. Conclusion: As a multimodal imaging contrast media, Conjugate-1 offers a promising imaging probe for tracking the delivery of EPCs in tumor models.