Acinetobacter baumannii (A. baumannii) strains are common nosocomial pathogens that can cause infections and can easily become resistant to antibiotics. Thus, analytical methods that can be used to rapidly identify A. baumannii from complex samples should be developed. Tail fiber proteins derived from the tail fibers of bacteriophages can recognize specific bacterial surface polysaccharides. For example, recombinant tail proteins, such as TF2 and TF6 derived from the tail fibers of bacteriophages ϕAB2 and ϕAB6, can recognize A. baumannii clinical isolates M3237 and 54149, respectively. Thus, TF2 and TF6 can be used as probes to target specific A. baumannii strains. Generally, TF2 and TF6 are tagged with a hexahistidine (His6) for ease of purification. Given that His6 possesses specific affinity toward alumina through His6-Al chelation, TF2- and TF6-immobilized alumina-coated magnetic nanoparticles (Fe3O4@Al2O3 MNPs) were generated through chelation under microwave heating (power, 900 W) for 60 s in this study. The as-prepared TF2-Fe3O4@Al2O3 and TF6-Fe3O4@Al2O3 MNPs were used as affinity probes to trap trace A. baumannii M3237 and 54149, respectively, from sample solutions. Matrix-assisted laser desorption/ionization mass spectrometry capable of identifying bacteria on the basis of the obtained fingerprint mass spectra of intact bacteria was used as the detection tool. Results demonstrated that the current approach can be used to distinguish A. baumannii M3237 from A. baumannii 54149 by using TF2-Fe3O4@Al2O3 and TF6-Fe3O4@Al2O3 MNPs as affinity probes. Furthermore, the limits of detection of the current method for A. baumannii M3237 and 54149 are ∼105 and ∼104 cells mL-1, respectively. The feasibility of using the developed method to selectively detect A. baumannii M3237 and 54149 from complex serum samples was demonstrated.