We previously used heavy-ion beam irradiation to generate a self-incompatible mutant of Verbena×hybrida ‘Temari Coral Pink’ (SC), which exhibits a late-acting self-incompatibility system. In the present study, the behavior of pollen tubes and seed productivity after self-pollination were comparatively investigated in SC and wild species Verbena peruviana (VP), one of the parental species of Verbena×hybrida. Although reciprocal cross-pollination between VP and SC produced seeds with high frequencies, namely 57.1% for SC×VP and 59.7% for VP×SC, self-pollinated VP flowers produced no seeds. In the latter, almost all of the pollen germinated on the stigma, but further growth of the pollen tube was inhibited at the upper part of the style. These observations of pollen tube behavior may indicate that the SI system of VP was different from that of SC. VP may possess a homomorphic gametophytic SI system, which is characterized by the inhibition of pollen tube growth at style. We propose a set of SC and VP as a novel model plants for genetic analysis of the SI mechanism in the Verbenaceae family.