This study investigated Aristaeomorpha foliacea, the exclusive species of Aristaeomorpha in the Mediterranean, Egypt, employing morphometric, molecular, and phylogenetic analyses. Morphometric assessments unveiled notable size variations between males and females, with males exhibiting a negative allometric growth pattern during spring. Utilizing COI and 16S rRNA genes, molecular analysis demonstrated congruence between morphometrically and molecular taxonomy. Phylogenetic insights revealed genetic relationships between A. foliacea populations from Egypt, Portugal, Italy, Malta, and China, suggesting a migratory pattern from the Atlantic to the Mediterranean. The study identified a moderate genetic diversity in A. foliacea, with six haplotypes in both COI and 16S rRNA regions, providing evolutionary insights. The integration of morphometric identification and phylogenetic study proved instrumental in elucidating the evolutionary relationships of this shrimp species. This interdisciplinary approach contributes valuable morphometric information for fisheries management, emphasizing the need for combined morphometric and DNA-based assessments for effective species identification and conservation. The research enhanced our understanding of A. foliacea in the Mediterranean, emphasizing the necessity for comprehensive approaches to species characterization and conservation.