Fluctuating asymmetry study on the body shapes of Nemipterus japonicus in Surigao River, Surigao del Norte was conducted to indicate the environmental and aquatic condition in the area. Thirty four samples of N. japonicus were gathered, upon sexing there were 19 females and 15 males were sampled and collected. Threadfin Bream Fish was used in this study as a bio-marker due to their tolerance on pollution serving as sensitive markers of disturbances in the area based on their fluctuating asymmetry. In the study, thin-plate spline (TPS) series were utilized, landmark analyses were obtained and subjected to Symmetry and Asymmetry in Geometric Data (SAGE) software. Procrustes ANOVA showed that although individual symmetry depicts no significant difference, Sides (Directional Asymmetry) and Interaction (Fluctuating asymmetry) showed a highly significant difference (p < 0.0005*). Principal Component Scores display a high percentage of fluctuating asymmetry in male (81.34%) and female (65.62%) samples. The body shape and directional asymmetry of N. japonicus indicates their response to the changing environment. The morphological changes during the ontogeny of this species are associated to the snout length, trunk length and body depth that may be related as a change in feeding habit and adaptation to their environmental conditions. This suggests that FA positively correlated with the results and the fish’ FA was useful as a bio-marker of stress, concluding that Surigao River has a poor ecological status.