The development of probes for rapid and selective detection of peroxynitrite in vivo is of great importance in biological science. We investigate different photoinduced electron transfer (PIET) processes of two generations of peroxynitrite probes. Each has fluorescein and phenol moieties; one is conjugated by an ether linkage while the other is conjugated via an amine linkage. Using theoretical calculations, we demonstrated that the PIET in the probe with an ether linkage occurs from the benzoic acid to the xanthene moiety. In contrast, the PIET in the probe with an amine linkage occurs from the phenol moiety to the fluorescein. This suggests that better sensitivity can be accomplished in probes with an amine linkage than with an ether linkage. Following this model, we designed two novel peroxynitrite probes and simulated their detection capabilities in the near-infrared region.