This research was conducted to explore the effect of nickel-ferrites (NiFe2O4) nanoparticle on Streptococcal pyogenes genome at the lowest effective dose. A total of 25 streptococcal isolates were recovered from local sporadic clinical cases and identified at the species level. Five isolates were selected to be tested in this work. The nickel-ferrites nanoparticles (NFNPs) were synthesized following the sol-gel auto-combustion method and determined using Scan Electron Microscope, Fourier-transform infrared spectroscopy (FTIR) and X-Ray Diffraction to determine the morphological surface and crystal-element analysis respectively. Bacterial growth before and after beeing exposed to NFNPs was measured at 600 nm wavelength using optical density, In vitro assessment of DNA variation was performed using random amplified polymorphic DNA technique RAPD after 24 hours exposure to particles at two concentrations comparing DNA fingerprints of control bacterial cell. Five 10-mer oligoneucleotide primers gave reproducible bands however, primer OPS-11 had scored the largest number of bands (33). RAPD method was able to reveal variation in band profiles both for exposure groups and control bacteria and concentration60 µg/ml gave more genetic variability. We conclude that RAPD-PCR is a good screening method of genomic regions that have undergone alterations as a result of exposure to nickel ferrite nanoparticles. Nickel ferrite can act as double edged-sward against bacteria and further studies are needed.