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<i>Salicornia</i> is a highly taxonomically problematic genus due to the reduced morphological observable characters. Ten Eurasian species are currently recognized: <i>S. alpini</i>, <i>S. europaea</i>, <i>S. fruticosa</i>, <i>S. hispanica</i>, <i>S. lagascae</i>, <i>S. perennans</i>, <i>S. perennis</i>, <i>S. persica</i>, <i>S. procumbens</i>, and <i>S. pruinosa</i>. In addition, eleven subspecies are accepted, mainly based on their distribution areas. Along the Venetian coasts and in Sardinia, in the past, an endemic species called <i>S. veneta</i> was recognized, but this name was later synonymized with <i>S. procumbens</i> subsp. <i>procumbens</i>. The aim of the present research is investigating different Italian <i>Salicornia</i> populations by a molecular point of view, using the nuclear ribosomal external transcribed spacer ETS and the plastid <i>psb</i>A-<i>trn</i>H intergenic spacer. A particular focus is on the comparison between Venetian (including those occurring in <i>locus classicus</i> of <i>S. veneta</i>) and Sardinian <i>S. procumbens</i> and other Italian populations of this species. The molecular analyses based on the plastid marker highlight that the Italian <i>S. procumbens</i> populations form two well distinct groups. In particular, some of the Venetian (<i>Locus classicus</i> of <i>S. veneta</i>) and all the Sardinian specimens are genetically distinct (=plastid haplotype 1) from the other investigated populations (=plastid haplotype 2). This indicates that the <i>psb</i>A<i>-trn</i>H haplotype 1 glassworts represent a distinct entity, which we suppose to coincide with the former <i>S. veneta</i>. Therefore, we suggest to recognize this taxonomic entity at the subspecies rank, as <i>S. procumbens</i> subsp. <i>veneta</i> comb. and stat. nov. However, contrary to the results found with the plastid <i>psb</i>A<i>-trn</i>H intergenic spacer, the ETS locus does not show a separation into two distinct clades for <i>S. procumbens</i>, probably due to a different evolution of the two loci. Nevertheless, in the ETS phylogenetic reconstruction, the Sardinian specimens (=ribotypes 2 and 3) are placed, together with a Moroccan sample, in a subclade separated from all the other <i>S. procumbens</i>. These results suggest that the Sardinian populations can represent a subspecies/incipient speciation process, probably due to geographic isolation. In the light of this, morphometric analyses (k-means, MANOVA, PCA, DA, and Box-Plot) have been carried out on the Sardinian and Venetian populations to verify if this distinction is detectable also by a morphological point of view. The morphometric analyses highlight the existence of two groups, concerning both the nuclear and plastid trees. Six characters were found to be diagnostic.