This manuscript aimed to study the effect of co-exposure of both lead acetate and titanium dioxide nanoparticles (TiO₂ NPs) on the major histocompatibility complex (Mhc) region and 16S rRNA sequence in vivo. Twenty-four male albino Swiss mice have randomly separated into four groups; Group 1 (control): was received only distilled water. Groups 2-4 received lead acetate (400 mg/kg body weight, orally by gavage for 15 consecutive days) + either distilled water (orally), or ZnCl₂ (4 mg/kg body weight, intraperitoneal injection), or titanium deoxidize nanoparticles TiO₂ (200 mg/kg body weight, intraperitoneal injection) for additional 15 consecutive days, respectively. According to the results of 16S rRNA sequence that the highest P-distance value (0.002) found between control group and both (lead acetate and lead acetate+TiO₂)-treated groups which reflected the genetic effects of both lead acetate and TiO₂ NPs. The results of microsatellites revealed that the exposure to lead acetate affected the genetic structure, where the genetic similarity between control group and lead acetate-treated group was 0.83, while zinc chloride decrease lead acetate-induced genotoxicity where the genetic similarity was 0.88 comparing to the control group. Moreover, the co-exposure to lead acetate and TiO₂ NPs led to more genotoxicity and DNA damage, that is clear in the genetic similarity between control group and lead acetate+TiO₂-treated group which was 0.74.