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This study presents a subcellular DNA barcoding system for high\u2010throughput in vivo screening of mitochondrial\u2010targeting gold nanoparticles (NPs). After validating the robustness of the barcode system with six PEG\/TPP\u2011modified NPs in vitro, the materials library expands to 30 NP species differing in shape, size, and ligand. Their biodistributions are systematically evaluated across subcutaneous, orthotopic, and contralateral tumor models at organ, cell\u2010subtype, and mitochondrial levels. This multiplexed approach yields more than 1000 data points on in vivo nanoparticle uptake and targeting behaviors, while requiring 30\u2010fold fewer mice than conventional approaches. 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