Abstract Background and Aims Species delimitation can be challenging when analysing recently diverged species, especially those taxonomically synonymized owing to morphological similarities. We aimed to untangle the relationships between two grassland species, Petunia guarapuavensis and Petunia scheideana, exploring the dynamics of fast divergence and addressing their species delimitation. Methods We used a low-coverage genome sequencing and population genomic approach to distinguish species and populations between P. guarapuavensis and P. scheideana. Our analysis focused on detecting structuration, hybridization/introgression and phylogenetic patterns. We used demographic models to support species delimitation while exploring potential phylogeographical barriers influencing gene flow. Key Results Our findings indicated differentiation between the two species and revealed another lineage, which was phylogenetically distinct from the others and had no evidence of gene flow with them. The presence of a river acted as a phylogeographical barrier, limiting gene flow and allowing for structuration between closely related lineages. The optimal species delimitation scenario involved secondary contact between well-established lineages. Conclusions The rapid divergence observed in these Petunia species explains the lack of significant morphological differences, because floral diagnostic traits in species sharing pollinators tend to evolve more slowly. This study highlights the complexity of species delimitation in recently diverged groups and emphasizes the importance of genomic approaches in understanding evolutionary relationships and speciation dynamics.