One important outcome of biological introductions is to bring into contact species that diverged in allopatry. For interfertile taxa, 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. In this context, the recent secondary contact between the non-native species Ciona robusta and the native species C.intestinalis, in the English Channel, provides an excellent case study to examine. By means of a population genomic approach, using 310 SNPs developed from full transcriptomes, the genetic diversity at population and species level was examined by studying 449 individuals (NC.robusta = 213, NC. intestinalis = 236) sampled in 12 sites from the English Channel, North Sea, NW Atlantic and SE Pacific where they are found either alone or living in the same locality and habitat (syntopy). As expected from previous analyses, C. robusta showed less polymorphism than C. intestinalis, a pattern that may partly be explained by its non-native status in most of the study localities. The results clearly showed an almost complete absence of contemporary gene flow between the two species in syntopic localities, with only one first generation hybrid and none other genotype compatible with recent backcrosses. Interestingly, introgression was also observed in allopatric populations of both species (i.e. where no contemporary hybridization can occur). Furthermore, one allopatric population sampled in SE Pacific exhibited a much higher introgression rate compared to all others C. robusta populations. Altogether, these results indicate that the observed inter-specific gene flow is the outcome of historical introgression, spread afterward at a worldwide scale. They also point out that efficient barriers are preventing hybridization in the wild between the introduced and native species in the English Channel, thus making adaptive introgression of the introduced species unlikely to favor the sustainable establishment of the study non-native species.