Analysis of population genetic structure can contribute to our understanding of the ecology and evolution of organisms and inform conservation and resource management policies. Anguilla is a genus of freshwater eels containing 19 taxa (species and subspecies) many of which are experiencing population declines due to overharvesting, habitat degradation, and climate change. As some Anguilla species are important fisheries resources it is essential to determine the genetic structure of species to understand the boundaries of the fisheries stock/management units and help manage them appropriately. We performed a literature review of studies on the genetic structure of taxa in the genus Anguilla and conducted meta-analyses based on the mean and standard deviation of pairwise genetic differentiation values that were extracted from the tables and/or figures of 63 studies. We used subgroups and meta-regression to assess the influence of genetic marker, measure of differentiation, sample size, and sampling range on the degree of genetic differentiation detected. We found overall support for panmixia in Anguilla taxa, except for Anguilla marmorata. However, some taxa remain understudied and may also exhibit population genetic structure. Future studies should focus on filling gaps in sample size and sample representativeness to provide more accurate estimates of population genetic structure and improve our understanding of this enigmatic group.