Biomphalaria pfeifferi snails serve as the major intermediate host for intestinal schistosomiasis in Sudan. The genetic structure and infection status of 163 B. pfeifferi collected from six localities in Gezira State, Sudan (East Gezira, Greater Wadmedani, Hasahisa, North Umelgura, South Gezira, and Managil) were characterized. Cytochrome oxidase subunit I (COI) and 16S ribosomal RNA (16S rRNA) mitochondrial genes were used for B. pfeifferi molecular identification and genetic diversity investigation. Schistosoma mansoni infection was detected using the traditional cercarial shedding and molecular methods (Sm^F/R primers). Five COI haplotypes and ten 16S haplotypes were identified, with haplotype diversity of 0.50 for COI and 0.11 for 16S. High evolutionary divergence was observed between groups (Fst = 0.94) for the COI, and low genetic divergence (Fst = 0.04) for the 16S, indicating genetic divergence among Sudanese B. pfeifferi, with the 16S showing lower divergence than the COI, consistent with a post-bottleneck population expansion. Cercarial shedding detected an overall infection prevalence of 3.6% (8/219), with only two snails from Hasahisa shedding S. mansoni cercariae. The Sm^F/R primers revealed a higher infection prevalence of 7.4% (12/163), with all S. mansoni positive samples found at the Hasahisa site. Findings highlight the value of molecular diagnostic tools for accurate surveillance and emphasize the need for site-specific control strategies.

Biomphalaria pfeifferi is a key intermediate host for Schistosoma mansoni transmission in Sudan. In total, 27 complete mitochondrial genomes from seven B. pfeifferi populations in Gezira State, Sudan, were sequenced for the first time to investigate their population structure and phylogenetic relationships. This involved comparing the nucleotide composition, codon usage, rRNAs, and tRNAs of the East Gezira (EG), South Gezira (SG), Hasahisa (HA), Greater Wad Medani (GW), Managil (MA), and North Umelgura (NU1, NU3) populations. All 27 mitogenomes (13,688–13,696 bp) contained 37 genes with conserved AT/GC content (76.7/23.4%). Phylogenetic analysis revealed that although samples clustered within the same clade, B. pfeifferi from EG, SG, NU1, and NU3 grouped closely with B. pfeifferi from Kenya, whereas HA and GW samples formed distinct ancestral lineages. The MA population exhibited unique genetic characteristics, supported by phylogenetic trees and nucleotide/amino acid identity, suggesting the potential presence of a distinct B. pfeifferi subspecies that warrants further investigation. All protein-coding genes evolved under negative selection, with the amino acids of nad1 and nad6 being highly conserved, while nad3 exhibited some variation. Further research on the mitogenomic diversity of B. pfeifferi and other Biomphalaria species in Sudan and across Africa is needed in order to better understand the population structure and evolutionary history of Biomphalaria.