Parasite composition can be affected by physiological and ecological changes during host ontogeny. Intertidal fish do not travel long distances and live in the same area throughout their lifetimes, meaning that parasite communities can differ across geographic ranges. The objective of this study was to analyse the parasite communities of three fish species (Hypsoblennius sordidus, Helcogrammoides cunninghami and Scartichthys viridis) collected from the Chilean coast. The composition of parasite species was compared among host ontogenetic stages (larvae, juveniles and mature fish) and geographic areas. A total of 184 larval, 252 juveniles and 217 mature individuals were collected in the northern area (c. 24°S), and 186 larval, 192 juveniles and 112 mature individuals from the central area (c. 33°S). Ectoparasites were most prevalent in fish from the central area, whereas endoparasites were most prevalent in the northern area. The parasite species richness varied significantly between geographical areas for H. sordidus and H. cunninghami, but the parasite composition varied significantly between geographical areas for all fish species analysed. Therefore, the geographical area was the most important factor determining the parasite composition of intertidal fish species. The absence of endoparasites in fish larvae and the increased infestation in juvenile and mature fish may be explained by the shift in habitat from the water column to intertidal pools where prey abundance and availability are higher. On the other hand, hydrographic barriers affecting prey distributions may also offer an explanation as to the differences in parasite composition.