The metazoan parasites of the snapper,Pagrus auratus, collected in the Hauraki Gulf of New Zealand were surveyed and their distribution mapped and examined in relation to the age of the host. Nine species of ectoparasites and seven species of endoparasites were recorded and all were found to exhibit some degree of site‐specificity. The gill monogeneansLamellodiscus pagrosomiandBivagina pagrosomiwere found in well‐defined microhabitats on the gills.L. pagrosomiwas abundant on the middle section of the second gill arch and was found in greater numbers on the distal zone of the gill filaments of the external hemibranch. In contrast,B. pagrosomiwas particularly abundant on the first gill arch and on the basal zone of gill filaments of the external hemibranch. A third gill monogenean,Choricotyle australiensis, was found attached to the gill filaments in snapper of 3 years and older but was largely restricted to the buccal cavity in younger host fish. This suggests that site‐specificity may not be a static attribute but may alter along with other parameters of the host fish such as age and size. The gastro‐intestinal parasites were also found to exhibit habitat partitioning and segregation into specific niches with a highly site‐specific digenean,Diphtherostomumsp., occurring almost exclusively in the lumen of the rectum.