Shelled coiled pteropods are important indicators of the effect of ocean acidification. We aim to gain insight into their evolutionary potential to future conditions by observing spatial population structure and barriers to dispersal. Based on a fragmented assembly of Limacina bulimoides, we designed probes that can be used to assess patterns of diversity across the genome. We tested applicability of these probes across related species of pteropods: Limacina trochiformis, Limacina lesueurii, Limacina helicina and Heliconoides inflatus.