<p>The Bigeye scad (<i>Selar crumenophthalmus</i>) is an ecologically and economically important small pelagic species in Philippine fisheries, yet its stock structure in Northern Mindanao remains poorly understood. This study assessed populations from Murcielagos, Iligan, and Macajalar Bays using a combination of traditional morphometrics, meristic counts, and shape-based analyses of both fish bodies and sagittal otoliths. Ninety male specimens were examined for 16 morphometric and eight meristic characters, and body outlines were analyzed using elliptic Fourier methods. A total of 180 sagittal otoliths were measured for 13 morphometric parameters and subjected to shape analysis. Significant differences in body and otolith size metrics (<i>p</i> &lt; 0.05) were found, with individuals from Macajalar Bay generally larger, while meristic counts remained consistent across bays. No significant divergence was observed in overall fish body or otolith shape (<i>p</i> &gt; 0.05), although subtle variation in otolith circularity and squareness (<i>p</i> &lt; 0.05) likely reflects ontogenetic scaling rather than population-level differentiation. Size variation is therefore attributed to local growth conditions, age composition, and potential seasonal aggregation, with Macajalar Bay potentially functioning as a feeding or spawning aggregation site. These results indicate that <i>S. crumenophthalmus</i> in Northern Mindanao represents a single morphologically cohesive stock. The findings underscore the importance of integrated, region-wide management strategies for sustainable exploitation of resources. Future studies incorporating age determination, reproductive indices, and environmental monitoring are recommended to refine stock assessments and inform long-term fisheries management.</p>