In this paper, we used the distinguishable surface charge and mass of different bacterial strains for label free detection and differentiation of pathogen through impedance and magnetohydrodynamic (MHD) analysis. For the isolation of Escherichia coli and Staphylococcus aureus, functionalized magnetic nanoparticles (MNPs) were used. The proposed method is aimed at minimizing extensive chemical preparation and labor intensive conventional microbiological processing thereby reducing the detection time. Pathogens isolated from broth cultures using the MNPs were subjected to impedance rate measurement through an arduino-based automated impedance sensor along with differentiation on the basis of Larmor's motion through the MHD approach. The proposed method evidently reports that the two bacterial species bind differently to the MNPs giving appreciable variation in the impedance rate increment for a dc electric field of 250V/m. In addition to this, cross-field drift through 171.4 V/m electric field and a normal magnetic field of 500 Gauss led to lump formation in S. aureus but had no such effect on E. coli. The mobility analysis of the two species of bacteria was also carried out by observing the gyration of bacteria through naked eyes. The mobility of lumped bodies of S. aureus was of the order 10-10 m2/V sec; whereas for dispersed E. coli, it was 10-08 m2/V sec.