Nanoprobes with multiple imaging modality have attracted a great deal of attention due to the capability of offering complementary information from each individual component. This work presents a hybrid approach to synthesize manganese doped near infrared (NIR) emitting quantum dots. The Mn-doping process was accomplished in aqueous phase followed by a phase transfer to organic phase for ZnS coating. This bimodal nanoprobe displayed high NIR luminescence quantum yield (~14%) and capability of magnetic resonance imaging (MRI) (1.44 mM-1 s-1). The RGD-targeted nanoprobes have been exploited for in vitro cell labelling, in vivo tumor targeting and lymph node mapping. In addition, no adverse toxic effects were observed, demonstrating the high biocompatibility of this nanoprobe.