The Jaera albifrons species group of intertidal isopods is characterised by strong sexual isolation mediated by female discrimination against heterospecific male tactile-stimulatory courtship behaviour. This is the first study to examine the genetic basis of traits involved in tactile mediated sexual isolation. To determine the genetic architecture of male secondary sexual characters (species-specific hair traits carried on the legs of males and a carpus leg-segment shape difference) associated with sexual isolation, experimental hybrid populations of J. albifrons and J. ischiosetosa were used to construct AFLP-based genetic linkage maps. A number of chromosomal differences (Robertsonian fusions) between the parental species were shown to be associated with reduced hybrid fertility. A quantitative trait locus (QTL) mapping study revealed that the number of hairs and carpus shape have a complex genetic basis, involving a number of QTL showing dominance, epistasis and possible pleiotropic effects. These QTL mapped largely to putative regions of restricted recombination, especially chromosomal rearrangements. The qualitative difference, however, was shown to be controlled by a single (or several closely linked ) QTL that did not map to a region of restricted recombination. These findings suggest that introgressive hybridisation played an important role in speciation in the J. albifrons species group and that chromosomal rearrangements allowed incipient species to persist in the face of ongoing gene flow. The extensive sharing of a single 16S rDNA mitochondrial haplotype supports the assertion that gene flow has been important. The reinforcement of premating isolating by natural selection against costly hybridisation is suggested as the mechanism of speciation between these species. The complete dominance of the J. albifrons allele at the QTL controlling the qualitative difference between the species supports this model of speciation.