This study assessed morphometric indices of Oreochromis niloticus from Ugbo and Mahin coastal waters in Ilaje, Ondo State, Nigeria. A total of 120 specimens were collected, and 25 linear measurements were recorded. Data were analyzed using Student’s t-test and Principal Component Analysis (PCA). The results revealed negative allometric growth (b = 1.92–2.30), indicating slimmer body shapes with increasing length. Condition factors (1.93 ± 0.24 to 2.03 ± 0.46) suggested healthy populations. Significant morphological differences were observed in head diameter, length of anal fin base, pre-pelvic fin length, and pre-anal length (p < 0.05). PCA explained 76.8% of total morphometric variation, with greatest divergence in the head, body, and caudal regions, highlighting phenotypic plasticity in response to local environmental conditions. These findings provide baseline data for monitoring O. niloticus populations and offer practical guidance for fisheries management, including setting size limits, implementing size-selective harvesting, and prioritizing habitat conservation to maintain healthy and sustainable coastal fish populations.