Biological introductions bring into contact species that can still hybridize. The evolutionary outcomes of such secondary contacts may be diverse (e.g. adaptive introgression from or into the introduced species) but are not yet well examined in the wild. The recent secondary contact between the non-native sea squirt Ciona robusta (formerly known as C. intestinalis type A) and its native congener C. intestinalis (formerly known as C. intestinalis type B), in the western English Channel, provides an excellent case study to examine. We developed a panel of 310 ancestry-informative SNPs developed from a population transcriptomic study. Hybridization rate was examined by studying 449 individuals sampled in 8 sites from the sympatric range and 5 sites from allopatric ranges. The results clearly showed an almost complete absence of contemporary hybridization between the two species in syntopic localities, with only one first generation hybrid and no other genotype compatible with recent backcrosses. Despite lack of contemporary hybridization between the two species, shared polymorphisms were observed in sympatric and allopatric populations of both species. Furthermore, one allopatric population from SE Pacific exhibited a higher rate of introgression compared to all other C. robusta populations. Altogether, these results indicate that the observed level of shared polymorphism is the more probably the outcome of ancient gene flow spread afterwards at a worldwide scale. They also emphasise efficient reproductive barriers preventing hybridization between introduced and native species; this suggests that hybridization should not impede too much the expansion wave of the non-native species in its introduction range.