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 characterized using SEM, FT-IR and XRD to determine the surface morphology, elemental analysis and crystallinity respectively. The growth of bacteria before and after been 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 screen variation in band profiles both for exposure groups and control bacteria.