Parasite species have been widely used as fish host migration tag or as indicators of local pollution. In this paper our approach is to consider the entire parasite community as a biological indicator of the fish environmental conditions. Seven fish species belonging to the Apogonidae, Apogon bandanensis, A. cookii, A. doderleini, A. norfolkensis, A. trimaculatus, Cheilodipterus quinquelineatus and Fowleria variegata, were sampled on six stations in two bays (Grand-Rade and Sainte-Marie) around Nouméa (New-Caledonia). The two bays are submitted to urban wastewater inputs alone or combined with additional industrial inputs which influences decrease from the inner part to the entrance of each bay. A total of 592 fish were dissected for macro parasite examination. Parasites were grouped according to their taxonomical rank and development stage for the analysis. We found an inconsistent effect of the confinement between the two bays, revealing that the parasite community is not the same in the two bays. Moreover, the encysted metacercariae found in the pericardic cavity were found to be significant indicators of the specific anthropogenically impacted environmental conditions prevailing in the inner parts of the two bays. Other parasite taxa were found to be significant indicators of specific environmental conditions in one or two stations among the six sampled. Results on parasite specificity and biological life cycle of the parasite taxa found in sampled Apogonid were further compared with environmental parameters.