Ten isolates belonging to Proteus spp. were collected and obtained from Department of Biology, College of Science, the University of Baghdad. The diagnosis was done by polymerase chain reaction (PCR) technique using 16S rRNA gene and urease C gene. All isolates (100%) were sensitive to meropenem, imipenem, ciprofloxacin, gentamycin, amoxicillin, clavulanic acid and levofloxacin. These isolates also showed 60% sensitivity to cefixime and nitrofurantoin. However, both species of P. mirabilis and P. vulgaris showed the lowest sensitivity when treated with tetracycline (60%) and amikacin (20%). Cephalothin had a variable effect on the species under study as P. mirabilis isolates were 100% sensitive in comparison with the 80% sensitivity of P. vulgaris isolates. The antibacterial activities of Ag and TiO₂ nanoparticles (NPs) were investigated. The minimum inhibitory concentration (MIC) value of Ag NPs against both species isolates was 10 mg/mL, while the MIC value of TiO₂ NPs was 14 mg/mL against P. mirabilis and 15 mg/mL against P. vulgaris isolates. P. mirabilis isolates showed larger swarming diameter than P. vulgaris, but this motility phenomenon of P. vulgaris was arrested rapidly after incubation with sub-MIC of TiO₂ NPs and Ag NPs comparatively with control. All isolates showed shifting to down-regulation in the fliL gene expression under the effect of the NPs using TiO₂ NPs and Ag NPs. In conclusion, down-regulation of the fliL gene expression is directly linked to the inhibition of swarming movement of Proteus species. We encourage using these inhibitors (after tests to ensure minimal toxicity to human) in combination with antibiotics to ensure bactericidal /bacteriostatic effect to treat Proteus infections.