Peroxynitrite (ONOO-) is a highly reactive nitrogen species that plays pivotal roles in diverse physiological activities and pathological events. However, the sensitive and organelle-specific detection of ONOO- in complex biological environments remains a considerable challenge. In this study, we developed BMZ-ON, a novel near-infrared (NIR) "turn-on" fluorescent probe for the selective detection of mitochondrial ONOO-. Upon reaction with ONOO-, BMZ-ON undergoes a specific cleavage process to release BMZ-OH, accompanied by a marked enhancement of NIR fluorescence. The probe exhibited high sensitivity, with a detection limit of 95 nM, together with excellent selectivity toward ONOO- over other biologically relevant reactive species. In addition, co-localization studies demonstrated its effective mitochondrial targeting capability and good membrane permeability. BMZ-ON was further applied to visualize endogenous ONOO- fluctuations in living cells and zebrafish embryos. These results indicate that BMZ-ON provides an effective platform for monitoring mitochondrial ONOO- and may facilitate further studies on the involvement of ONOO- in mitochondrial dysfunction and related diseases.