Biological invasions can promote secondary contacts between related species and thus provide excellent case studies for investigating the joint ecological and evolutionary trajectories of interfertile taxa. Here, we studied two tunicates living in sympatry, and sometimes in syntopy, in the English Channel, Ciona intestinalis species A (presumed native to the NW Pacific) and species B (native to the N Atlantic). In addition to monitoring their co-existence over time, we examined the level of interspecific gene flow, a process that may increase the invasiveness of the non-native species. The sampling scheme was repeated twice a year for 3 years (six distinct generations) to determine the relative abundance of the two species in 11 localities along the coasts of the English Channel and the Iroise Sea (covering 1600 km) in Brittany, France. We examined 23,000 individuals, including 5315 specimens for which reproductive status was determined. Four species-diagnostic molecular markers traced interspecific gene flow on a random subset of 3048 individuals. Regardless of the sampling date, the two species co-occurred in most of the study sites, with species A showing higher frequency in the autumn. The regional pattern of seasonal variation in relative abundance of the two congeners appears to correspond to different thermal growth optima. Abrupt variations in environmental parameters can act synergistically and may favor the non-native species locally. Despite syntopy, synchronous gamete production and successful in vitro interspecific crosses, only 4.3 % individuals showed an admixed genome (i.e. footprint of present-day or past introgression events), most of them with a species A maternal lineage, of which only one was a putative first generation hybrid. Altogether, efficient barriers seem to prevent interspecific crosses between the two interfertile congeners in the wild: present-day hybridization may have less impact than competitive interactions on the fate of the two study species over their sympatric range.