Background: The identification of foodborne pathogenic bacteria types plays a crucial role in food safety and public health. In consideration of long culturing times, tedious operations and the desired specific recognition elements in conventional methods, the alternative fluorescent sensor arrays can offer a high-effective approach in bacterial identification by using multiple cross-reactive receptors. Herein, we achieve this goal by constructing an upconversion fluorescent sensor array based on anti-stokes luminogens featuring a series of functional lanthanide-doped upconversion nanoparticles (UCNPs) with phenylboronic acid, phosphate groups, or imidazole ionic liquid. The prevalent spotlight effect of microorganism and the electrostatic interaction between UCNPs and bacteria endow such sensor array an excellent discrimination property. Results: Seven common foodborne pathogenic bacteria including two Gram-positive bacteria (Staphylococcus aureus and Listeria monocytogenes) and five Gram-negative bacteria (Escherichia coli, Salmonella, Cronobacter sakazakii, Shigella flexneri and Vibrio parahaemolyticus) are precisely identified with 100% accuracy via linear discriminant analysis (LDA). Furthermore, blends of bacteria have been identified accurately. Bacteria in real samples (tap water, milk and beef) have been effectively discriminated with 92.1% accuracy. Conclusions: Current fluorescence sensor array is a powerful tool for high-throughput bacteria identification, which overcomes the time-consuming bacteria culture and heavy dependence of specific recognition elements. The high efficiency of whole bacterial cell detection and the discrimination capability of life and death bacteria can brighten the application of fluorescence sensor array.