The present study is the first investigation on ectoparasites of commercial important fish from Segara Anakan, a brackish water lagoon located at the southern coast of Java, Indonesia. Eight economically important marine fish species (Mugil cephalus, Siganus javus, Scatophagus argus, Caranx sexfasciatus, Lutjanus johnii, Eleutheronema tetradactylum, Johnius coitor, and Epinephelus coioides) were examined for crustacean parasites. Prevalence and intensity data for each parasite species are given, together with an analysis of the origin and possible transmission pathways. A highly divers copepod fauna consisting of 23 different species and two isopods was found. All fish species were at least infested with two copepod species, with the exception of L. johnii, S. argus, and M. cephalus. With seven and six species, respectively, they harboured the most species-rich ectoparasite fauna. The copepods Ergasilus sp. 3 and Caligus acanthopagri on S. argus showed the highest prevalence (78.6) and intensity [17.8 (1-233) and 5.3 (1-22)] of infestation. The recorded parasite fauna is represented by marine, brackish water, and probably also freshwater components. The brackish water environment of Segara Anakan does not prevent disease outbreaks due to parasitic copepods by preventing pathogenic marine or freshwater species to enter the lagoon. This might cause fish health problems if the Segara Anakan Lagoon would be developed for finfish mariculture in future.