The lateral line distribution is an important morphological feature for taxonomic differentiation within the genus Cynoglossus. This study documents a rare lateral line anomaly in Cynoglossus quadrilineatus, a species typically characterized by two ocular-side lateral lines. A specimen with three well-developed ocular-side lateral lines was discovered in coastal waters near the Andaman and Nicobar Islands, India. Morphological and molecular analyses, including a direct comparison between anomalous and non-anomalous specimens, were conducted to determine whether the anomaly represents a taxonomic feature or a developmental variation. Meristic and morphometric assessments confirmed that the anomalous specimen falls within the diagnostic range of C. quadrilineatus. Cytochrome c oxidase I (COI) gene analysis revealed minimal genetic divergence (0.48%) between specimens with two and three ocular-side lateral lines, supporting their conspecificity. These findings suggest that the additional lateral line is a developmental anomaly rather than a species-specific trait, demonstrating that lateral line variations can occur in C. quadrilineatus, despite being a critical morphological character in species diagnosis. This conclusion is based on a single individual exhibiting the anomaly, which limits broader generalization and emphasizes the need for additional observations. This study highlights the importance of integrating molecular tools with traditional taxonomy to resolve uncertainties arising from morphological deviations in fish species.