ddRAD-Seq1 and target capture2 sequencing methods have widely been used to explore a range of population and phylogenetic questions3 including historic samples4. ddRAD-seq methods result in large amounts of missing data compared to target capture due to allelic dropout (especially when comparing across species) and requires very high quality DNA5. Even though most target enrichment methods strongly rely on pre-existing transcriptome or genome resources, such data are still scarce or poorly annotated for the Jasus genus and closely related species. The Jasus clade encompasses economically important lobster fisheries around the Southern Hemisphere. These species have some of the longest planktonic larval stages (1-2 years), which can be transported over long distances6. Here, we tested a target enrichment approach based on a set of loci discovered in ddRAD-seq libraries of Jasus edwardsii and Sagmariasus verreauxi to investigate the role of adaptation and self-recruitment processes underlying diversification in a range of Jasus species. A total of 2,241 probes were designed to target specific regions in contemporary and historic specimens (museum-collection) from J. caveorum, J. edwardsii, J. frontalis, J. lalandii, J. paulensis and J. tristani. The method efficiency was evaluated with respect to number of targets successfully recovered across species, which varied from 671 for J. frontalis to 1,308 for J. tristani. Only 279 were shared across all valid individuals from the six species. Patterns of mismatches (C to T and G to A substitution bias) resulting from DNA damage were compared between historic and contemporary samples enabling further data filtering. Our results show the feasibility of integrating two genomic methods to enrich genetic data for which no reference genome nor transcriptome are available. Moreover, the methods we employed were successfully applied to museum collection samples, which are unique resources to compare progressive changes in genetic diversity in lobster populations over time.