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A highly sensitive electrochemiluminescence (ECL) biosensing method was developed for monitoring casein kinase Ⅱ (CK2) at subcellular level via bio-bar-code assay. A bio-bar-code probe (h-DNA/AuNPs/p-DNA) prepared by conjugating phosphorylated DNA (p-DNA) and hairpin DNA (h-DNA) onto gold nanoparticles (AuNPs) was used as a carrier for ECL signal reagent (Ru(phen)32+) while a specific peptide was used as a recognition substance. A gold ultramicroelectrode with a diameter of 400 nm was fabricated and then modified with the specific peptide via self-assembly technique to obtain peptide modified gold ultramicroelectrode. The peptide on gold ultramicroelectrode was phosphorylated in the presence of CK2 and adenosine 5′-triphosphate, and then the phosphorylated peptide was integrated with the h-DNA/AuNPs/p-DNA through a process mediated by zirconium cations (Zr4+), and finally Ru(phen)32+was intercalated into h-DNA. A“signal on”ECL method was developed for the detection of CK2 in the range of 0.005–0.2 U/mL with a detection limit of 0.001 U/mL. Additionally, combined efficient subcellular phosphorylation in vivo with bio-bar-code-based ECL biosensing method, the ECL method was further applied to monitor CK2 at subcellular level without tedious subcellular fractionation. It was found that the concentration of CK2 by inserting the peptide modified gold ultramicroelectrode into the nucleus was higher than that into cytoplasm of HeLa cells. A distinct heterogeneity among CK2 concentrations in single cells was observed for cellular heterogeneity assessment.