Veronica subg. Pseudolysimachium is widely known and cultivated because of the large and dense inflorescences of its species. Their success as cultivated plant stems in part to the cross-compatibility across the subgenus and in the part to the wide ecological amplitude from species growing in wetlands to others growing in semi-deserts. Hybridization between species is believed to be frequent due to the large morphological variation and intermediate forms in sympatry of their putative parents. The Russian Altai is a center of diversity for the taxon and many hybrid taxa have been described there based on morphology. Here, we test these hybrid hypotheses using dominant SRAP markers. The method relies on primers anchored in open reading frames and amplifying intronic regions, which are scored as fragment length polymorphisms. Using seven primer pairs, we analyzed 63 loci without missing data. Our data support a close relationship of V. × grisea, V. × schmakovii and V. taigischensis with V. longifolia but influence of the other suggested parents V. incana, V. porphyriana, and V. pinnata is weak. Similarly, V. × sessiliflora shows strong genetic similarity with V. porphyriana but only weakly with V. pinnata. Overall, the methodology worked reliably and provided a large number of variable polymorphisms. The lack of support for the hybrid hypotheses is, therefore, considered to be due to still low number of loci and possible backcrossing with one of the parents.