Nile Tilapia (Oreochromis niloticus) farming is common in Laguna Lake, Taal Lake and Sampaloc Lake. The main purpose of this study was to differentiate the morphology of Nile Tilapia in these lake, in terms of its external morphoanatomy including: size (length and width), weight, color of the skin, smell, and texture of the skin as well as its internal morphoanatomy which includes: color of the meat, color of the organs, and color of the gills and taste using hedonic scale for sensory analysis. Geographical differences and several environmental factors influence the morphoanatomy of nile tilapia living in the study sites. This was assessed through adapted dissection made by the researchers and boiling method for the sensory analysis. The characterization proved that there are external and internal morphological differences among the Nile tilapias. The results showed that Nile Tilapia, in Taal Lake had significantly pleasing external and internal morphological characteristics followed by the Sampaloc Lake, and lastly the most unpleasing and unpalatable of all is the Laguna Lake.