Praziquantel (PZQ) is currently the only drug recommended by the World Health Organization (WHO) for treating schistosomiasis, raising concerns about potential resistance. Frequent use of PZQ may reduce the genetic diversity of Schistosoma mansoni, affecting its adaptability and survival. The objective of this study was to test the impact of Praziquantel treatment and population bottlenecks on the genetic diversity of S. mansoni by experimental infection using a wild strain isolated from naturally infected rodents. Experimental infections were conducted in outbred mice, which were infected with 120 cercariae, and treated with two different doses of PZQ (3 × 150 mg/kg and 3 × 300 mg/kg) at 50, 51, and 52 days post-exposure, and necropsied 15 days later. Microsatellites and MT-CO1 were used as molecular markers. An 85.5 % reduction in parasite load (p = 0.04) was observed after 300 mg/kg PZQ treatment, with greater efficacy in male worms. MT-CO1 analysis identified two haplotypes differing by one polymorphic site, with one haplotype representing 84.2 % of the population. Low genetic differentiation was observed for MT-CO1. All seven microsatellite loci studied exhibited polymorphisms, with 3-7 alleles per locus. Praziquantel treatment caused population bottleneck, reduced genetic variability in both dosage groups: IT150 (R = 0.14043, p = 0.000) and IT300 (R = 0.13610, p = 0.005), and eliminated alleles with low initial frequencies. We concluded that microsatellite markers showed genetic differentiation with elimination of rare alleles, confirming the genetic bottleneck effect due to treatment with PZQ.