Biological invasions of parasites and their hosts are ideal to study coevolution in nature. Two closely related copepod parasites have invaded Eastern Atlantic mussels and oysters. Specialist Mytilicola intestinalis have invaded from the Mediterranean Sea and generalist Mytilicola orientalis from the inland sea of Japan. A transcriptomic backbone of these parasites will be generated as a genomic resource. Here we report the first results of these transcriptomic resources and present dN/dS ratios of homologous genes and polymorphism data. We expect to find neutral and selective markers for downstream applications and to find targets of selection. These could explain a parasitic and generalist versus a specialist life style