Sexual barriers associated with mate choice are often found to be associated with some level of ecological isolation between species. The independence and relative strength of sexual isolation are thus difficult to assess. Here we take advantage of a pair of marine isopod species (Jaera albifronsand J. praehirsuta) that show sexual isolation and coexist in populations where they share the same microhabitat or not (i.e. without or with ecological isolation). We estimated the strength of sexual isolation between J. albifronsand J. praehirsutausing no-choice trials and a multiple-choice experimental population. We found that sexual isolation is strong in both the presence and absence of ecological isolation, but that it is asymmetric and fails to prevent interspecific gene flow entirely. First-generation intrinsic post-zygotic barriers were low, and there was no sexual isolation within J. praehirsutaacross habitats. The J. albifrons/ J. praehirsutaspecies pair thus provides an example where the role of sexual isolation as a barrier to gene flow i) does not depend upon current ecological isolation, ii) seems to have evolved independently of local ecological conditions, but iii) is insufficient to complete speciation entirely on its own.