Background: Pogonus littoralis and Pogonus chalceus are very close related species with quite different ecological preferences within salt marshes. We study the evolutionary processes in and between these presumably young species. Therefore, we compare the variation in ecologically relevant characters and the genetic variation within one of the species (intraspecific differentiation) with the variation of the two types of characters between the two species (interspecific variation). Data are compared between two independent sets of populations, one set at a small geographical scale (the ecologically diverse Guérande area in France) and the other set at a Atlantic-Mediterranean scale. Results: Body and relative wing size and IDHI allozyme data show that the intraspecific variation in P. chalceus is high and in the same range as the interspecific variation (P. chalceus versus P. littoralis). Based on neutral markers (other allozymes and mitochondrial DNA) on the other hand, the intraspecific variation in P. chalceus is much lower in comparison to the interspecific variation. Conclusion: The different ecotypes in the highly polytypic species P. chalceus are as highly differentiated in ecological characters as true species, but are not recognised as such by screening neutral DNA polymorphisms. This can be interpreted as a case of ongoing speciation driven by natural selection adapting each ecotype to its respective ecological niche. The same ecological process can be recognised in the differentiation between the two sister species, where en plus reproductive isolation between the two gene pools occurred, allowing independent drift and mutation accumulation in neutral genetic characters.