Abstract
BACKGROUND: Freshwater snails of the genus Biomphalaria include several species of major public health importance as intermediate hosts of schistosomiasis and represent a key group for evolutionary and taxonomic research within Hygrophila. However, complete mitochondrial genomes are available for only a limited number of Biomphalaria species, restricting comparative assessments of mitogenome evolution and the ability of mitogenomic data to resolve contentious relationships within Planorbidae and across Hygrophila. Here, we generate and analyse six complete mitochondrial genomes from four Neotropical Biomphalaria species collected in Argentina, including the first mitogenomes for B. peregrina and B. orbignyi, and evaluate genomic architecture, molecular evolutionary patterns, and phylogenetic relationships using multiple mitogenome-based approaches. RESULTS: All six mitogenomes contained the standard complement of 37 mitochondrial genes and exhibited a fully conserved gene order and strand orientation across Biomphalaria. Genomes were highly compact, with numerous gene overlaps. An unusually long non-coding region (210–242 bp) was detected exclusively in B. peregrina, contributing to its slightly larger mitogenome size. Intraspecific variation in the secondary structure of tRNA(Cys), including arm truncation, was also observed within B. peregrina. All genomes showed negative AT-skew and positive GC-skew, indicating conserved strand asymmetry across Hygrophila. Protein-coding genes displayed strong codon-usage bias and were predominantly shaped by purifying selection, with atp8 identified as the most variable and least constrained gene. Phylogenetic analyses recovered two closely related topologies across datasets, supported monophyly of Bulinidae and Lymnaeidae, and consistently placed bulinids within planorbids, rendering Planorbidae non-monophyletic. Amphipepleinae was monophyletic, whereas Lymnaeinae was paraphyletic in a pattern sensitive to taxon sampling. Within Biomphalaria, B. peregrina was consistently resolved as the earliest-diverging lineage among sampled species. CONCLUSIONS: These six newly generated mitogenomes substantially expand genomic resources for Neotropical Biomphalaria and reveal strong conservation of mitochondrial genome organisation alongside pronounced heterogeneity in gene-specific evolutionary dynamics. Complete mitochondrial genomes enhance phylogenetic resolution within Hygrophila and provide independent evidence relevant to ongoing debates in planorbid systematics, including the affinity between Bulininae and Planorbinae. Nevertheless, broader taxon sampling and the integration of nuclear genomic data will be essential to fully resolve subfamilial relationships and species boundaries within this medically important group. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12862-026-02520-0.