This study highlights the synthesis of an antibody conjugated magnetic carbon nanotube bioprobe for the recognition and separation of Pseudomonas aeruginosa (P. aeruginosa), a gram negative bacterium, from its mixed culture with Staphylococcus aureus (S. aureus). Multiwalled carbon nanotubes containing iron oxide nanoparticles (magnetic carbon nanotubes) were synthesized in a single step by a spray pyrolysis method. The synthesized magnetic nanotubes were characterized by X-ray diffraction, electron microscopy and magnetic property measurements. A P. aeruginosa specific rhodamine-labelled goat anti-Pseudomonas antibody was covalently attached to the magnetic carbon nanotubes to develop a bioprobe. Raman and Fourier transform spectroscopy studies were carried out to confirm the attachment of the antibodies to the magnetic nanotubes. The designed bioprobe was employed for the capture and subsequent separation of P. aeruginosa from its mixed culture with S. aureus. The probing efficiency of the developed bioprobe was characterized and confirmed by culturing the captured P. aeruginosa in selective media followed by fluorescence and scanning electron microscopy studies. A time dependent increase in the capture efficiency of the bioprobe for P. aeruginosa was noticed and found to be 65% within five minutes of incubation. Thus, the designed bioprobe presents a simple, reliable and cost effective diagnostic tool for rapid identification and separation of a particular bacterium from a site of co-infection which is of immense clinical relevance.