This dataset contains the original plastid DNA sequences and cloned nuclear ITS sequences used to investigate natural hybridization between Verbascum virgatum and Verbascum sinuatum in southwestern Portugal. Dataset Contents Plastid DNA sequences (FASTA format) Cloned ITS sequences (FASTA format) Sequence alignments Metadata table including ID of samples Methods Overview DNA was extracted from leaf tissue and plastid and nuclear ribosomal ITS regions were amplified using standard protocols. ITS amplicons were cloned to resolve intra-individual polymorphism. Sequences were aligned and analyzed to infer maternal lineage and nuclear contributions from parental taxa.