Protecting marine isolated habitats is not enough to maintain biodiversity. The establishment of networks of marine protected areas is fundamental to enhance species resilience in front of environmental disturbances (Botshford el al., 2009). Population connectivity refers to the exchange of individuals among geographically separated subpopulations that comprise a metapopulation and is the base for building those networks. For most littoral marine organisms, with restricted adult movement, pelagic larvae represent the most important dispersal phase (Cowen el al., 2007). Thus, measuring marine connectivity, although important for the management of biodiversity, is not an easy task. Assessing genetic connectivity implies identifying gene flow; individuals that disperse, even over long distances, but do not contribute with their genes to the next generation in the areas visited during their lifespan will not be relevant in ensuring the long term persistence of those populations. Genetic diversity and siruilarity among areas is a frequently used proxy of connectivity. Most studies of marine organisms have used this indirect approach based on classical population genetics comparing allele frequency distributions between populations (palumbi, 2003; Duran el al., 2004b; Carreras el al., 2007; Schunter el al., 2011b) and only a few studies have directly measured connectivity through parentage or sibship analyses (planes el al., 2009; Schunter el al., 2014). Population genetic studies on marine species have steadily increased in the last 20 years and the molecular markers used have changed through time and will continue doing so as new technological advances allow using them in non-model organisms (Milano el al., 2014; Shinzato el al., 2015). Several misconceptions, based on the use of different genetic markers, have arisen. They will be discussed using case examples from different marine organisms.