Connectivity is frequently cited as a vital component of Marine Protected Area (MPA) networks and was formally identified as one of five key principles for marine network design in European waters. Yet, without the ability to demonstrate connectivity, it is impossible to be certain that sites designated within a MPA network do in fact constitute a network, when they may –irrespective of the diversity and rarity of the taxa within them– be in reality a set of unlinked habitats and associated species assemblages. However, the process of assessing connectivity between MPAs, and which taxa to include in assessments of connectivity, is often difficult and can be dependent on a variety of factors that can be outside the control of managers, stakeholders and policymakers. Among the many methods that have been used to assess connectivity, genetic markers are often used to infer connectivity indirectly by estimating the degree of genetic differentiation between populations of a species or by inferring the origin(s) of migrants using assignment methods. While modern molecular methods can be extremely robust and are now routinely used to address conservation issues, genetic data are, to the authors’ knowledge, rarely used to inform designation of MPA networks. In this paper, several biological and methodological factors are highlighted, consideration of which may help to inform the selection of species for assessments of connectivity between MPAs in a network, and this paper suggests ways in which genetic data may be interpreted to inform MPA design and policy.