Specimens of Calanus finmarchicus, C. helgolandicus, C. glacialis and C. hyperboreus from various locations including areas of sympatry were sequenced with a protocol of target-capture to be analysed for signatures of inter-specific hybridization. Hybridization between species was initially inferred in Calanus with microsatellites. However, considering the technical issues associated with these microsatellites, a more powerful approach was necessary to shed light on this matter and determine whether these species hybridize in their sympatric areas. All the analyses performed using the sequenced datasets found no evidence for introgression among species.