The striped mullet Mugil incilis is an important fishery resource in the Colombian Caribbean, but its management has traditionally assumed a single uniform stock without empirical validation. This study evaluated phenotypic stock differentiation across three lagoon systems: Ciénaga Grande de Santa Marta (CGSM), Ciénaga de la Virgen (CVir), and Ciénaga de la Caimanera (CCera). A total of 196 individuals were collected (2023): 78 from CGSM (19.8–30.7 cm TL), 65 from CVir (17.0–37.8 cm TL), and 53 from CCera (17.5–30.0 cm TL). A truss network of 25 morphometric distances was standardized using allometric correction to eliminate ontogenetic effects. Multivariate analyses (PERMANOVA) revealed significant differences among lagoons, with pairwise comparisons confirming consistent separation. PERMDISP indicated that these differences were mainly due to body shape rather than within-group dispersion. Divergence was concentrated in three anatomical regions: cranial structures, trunk depth, and the mid-posterior/caudal peduncle, all related to feeding performance and swimming efficiency. SIMPER and univariate analyses identified these areas as the main contributors to stock differentiation. Classification models reinforced these findings: Flexible Discriminant Analysis achieved 86.9 % accuracy, while Multinomial Logistic Regression achieved 95 % accuracy with a pseudo-R² of 0.92. Both methods provided consistent evidence and strong predictive power, demonstrating the robustness of morphometric markers for stock discrimination. This is the first comprehensive evidence of at least three distinct M. incilis stocks in the Colombian Caribbean. Incorporating this differentiation into fisheries management is critical to reducing overexploitation risks and supporting sustainable strategies tailored to each lagoon’s specific dynamics.
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