Fe3O4 magnetic nanoparticles (MNPs) are promising candidates for various biomedical applications due to their extraordinary properties. Such MNPs, surface modified with chitosan-glutaraldehyde (Fe3O4-CH/GLD) i.e. magnetic core/shell nanostructures, were used in the present study to investigate isolation and enrichment of bacterial DNA. Isolation was carried out in comparison with an organic method. FTIR was used to confirm biding of DNA onto the surface of the core-shell structures. The concentration of isolated DNA (yield) was 14.90 and 17.55 μg mL-1 for phenol/chloroform and magnetic isolation methods, respectively. The purity of isolated DNA was found to be 1.69 and 1.71 for phenol/chloroform and magnetic isolation methods, respectively. The present study firstly reports the comparison between magnetic and organic isolation of DNA. From both results (yield and purity), it was found that magnetic isolation of DNA was superior to the general organic method used for bacterial DNA isolation. Experiments for DNA enrichment were performed in batch mode and the effects of core/shell concentration, pH of the sample solution and temperature were optimized. The formation energy required for adsorption of DNA was found to be -55.56 × 10-23 J per molecule (-34.70 × 10-4 eV per molecule). The negative value indicates energy was utilized (endothermic process) for the adsorption of DNA onto the magnetic core/shells. The magnetic isolation method used in the present study was simple, fast, robust and ecofriendly (it does not require organic solvents or sophisticated equipment).