Chanos chanos (milkfish) locally known as Bangus is the main aquaculture product of the Philippines. The status of bangus production in Zamboanga City declined from 2012-2016. Diseases in C. chanos were known to be caused by parasites and have remained an issue to fish farming. Some of the parasites have been discovered to have zoonotic potential in mammalian hosts including man making them of public health importance. In this study, the identification, intensity, prevalence and biometric relations of endoparasites in C. chanos were determined. A total of 120 juvenile bangus were collected in the wetlands of Zamboanga City from July 2016 to August 2016. There were 4 endoparasites identified namely: Ichtyobodo sp., Trichodina sp., Acanthocephalans spp. and Diphyllobothrium latum. The most prevalent was Ichtyobodo sp. (40%) and the least prevalent was D. latum (1.66%). Ichtyobodo sp. has the highest mean intensity (4.39) found in the gills and D. latum has the lowest mean intensity (0.2) found in the intestine. Pearson’s Correlation Coefficient Analysis revealed a negative correlation between fish length and number of endoparasites (-0.17), fish weight and number of endoparasites (-0.27) and body height and the number of endoparasites (-0.31). However, there were high correlations between fish length and fish weight (0.78), fish length and fish height (0.61) and fish weight and fish height (0.73).