Studying the population genetics of a parasite species provides insights into the ecological and evolutionary implications for the host–parasite interactions. In this context, this chapter provides an overview of the genetic and molecular approaches applied to study the genetic variation of aquatic helminth parasites and their advantages and disadvantages in resolving their genetic structure over spatial scales. It then explores the investigations into parasite and host traits that influence the shape of the observed genetic population structure of certain parasite species. The spatial structure of a parasite population may also reflect the population genetic structure of its hosts; in this regard, examples of congruence and incongruence between the genetic population structure of the two interacting organisms are presented. Additionally, future trends, such as the genome-wide approach in estimating and understanding genome-scale variability in parasite populations, that is, population genomics, are discussed. Population genomics will enable addressing of the microevolutionary aspects of parasite–host associations and gaining of insights into adaptive coevolutionary processes of parasite species at the ecological level.