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Dominating global arid environments, from desert to coastal dunes, most Tenebrionidae are highly specific in their habitat preferences and display limited dispersal potential, thus exhibiting a remarkable degree of regional genetic and morphological differentiation. The tenebrionid genus Phaleria is speciose and widely distributed, with P. acuminata and P. bimaculata having a wide Mediterranean distribution, with numerous morphological differentiations at population level, often described as different taxa of doubtful taxonomical significance. In order to investigate the variability of the central Mediterranean populations of P. bimaculata and P. acuminata and to compare the results obtained with different identification techniques, these species were sampled on sandy beaches in Sicily (southern Italy) and on circum-Sicilian and Maltese islands. Collected samples were studied through the application of geometric morphometrics and the sequencing of a fragment of the mitochondrial COII gene. Geometric morphometrics and molecular analyses gave congruent results, allowing a sound separation of the two species. At the population level, the two species showed different patterns. P. acuminata showed a remarkable morphological and molecular homogeneity throughout the sampled area. Conversely, two well-characterized sub-clades were detected within P. bimaculata, and within the two lineages, a low-to-absent inter-populations differentiation was observed, in spite of the physical isolation of the sampled sandy beaches and of their geographical distance. These two P. bimaculata lineages, hereby named "Tyrrhenian sub-clade" and "Southern sub-clade," might be compatible with the hypothesis of subspecific status already proposed for the populations from the Aeolian archipelago (as P. bimaculata marcuzzii Aliquo).