Veronica subgen. Pseudolysimachium constitutes a group of about 28 species across northern Eurasia, many of them with considerable intraspecific morphological variation. This intraspecific variation may be due to large geographical distribution area, wide ecological amplitude, or widespread hybridization and polyploidization. Several recent studies using molecular data have shown that hybridization as an explanation for generating evolutionary novelties and high intraspecific variation may be more common than previously thought. Here we investigate the importance of hybridization in generating morphological variation and blurring species boundaries in V. subgen. Pseudolysimachium using analyses of cpDNA sequences from 139 individuals from 18 species and ten putative hybrids, and pyrosequenced ITS1 nrDNA sequences from 37 individuals from 16 species and four putative hybrids. In addition, we estimated ploidy levels for 42 individuals of ten species and five putative hybrids using flow cytometry. Analyses of cpDNA did not resolve phylogenetic structure (most of the species were polyphyletic). Our second approach, pyrosequencing of ITS1, generated up to nine different unique sequences per individual and phylogenetic analyses of the dataset resolved some basal nodes but, again, species were often non-monophyletic. The results are most compatible with a scenario of an East Asian origin and repeated spread across Pleistocene Eurasian steppes, known as important plant diversification center, with frequent interspecific hybridization. We compare the applicability of these molecular regions for resolving hybridizing species complexes and specifically address hypotheses of hybrid origins for several species within the subgenus. However, any population genetic, phylogeographic or other analysis of evolutionary questions in one species alone would be futile without considering introgression from related species.