We performed a field experiment in the Westerschelde Estuary (The Netherlands) to characterize the colonization dynamics of nematodes in relation to the proximity of a source population and to local environmental conditions. The effects of colonization on the population genetic structure of the dominant species, Pellioditis marina, were simultaneously investigated. Two contrasting sites, each containing four patches with defaunated algae, were sampled seven times during 1 month. Site A was situated amidst Fucus stands, which permanently harbor P. marina, while site B was approximately 100 m from any source population and experienced more stressful environmental conditions. We hypothesized that (1) colonization in site A would proceed faster than in site B and that (2) founder events and genetic bottlenecks would affect population genetic structure and differentiation at site B more than at site A. We screened 992 individuals for variation in 426 base pairs of the cytochrome oxidase c subunit 1 gene with the single-strand conformation polymorphism method. The algal deposits at site A were indeed more rapidly colonized and reached fivefold higher densities of nematodes than those in site B. Haplotype composition in site A was very similar to that of the source population, while rare haplotypes were abundant and genetic diversity was lower in site B. We conclude that founder effects and genetic bottlenecks structured the populations in site B. The genetic differences between patches in each site further indicate that effective migration in P. marina is low and that priority effects influence the genetic structure of P. marina populations.