The genus Salicornia (Amaranthaceae) was established by Linnaeus. Commonly known as ‘glassworts’, the species of the genus are articulated succulent herbs with cortical palisade, opposite decussate scale-leaves, thyrsoid cymes, flowers packed in cauline depressions and the diaspore composed of l-seeded utricle. Therefore, due to the importance of the plant species, we performed a combination of morphological and molecular data analyses on this species. A total of 72 randomly collected plants from 8 natural populations in 2 provinces were evaluated using ISSR markers and morphological traits. Analysis of molecular variance (AMOVA) test revealed significant genetic difference among the studied populations, and also showed that 45% of total genetic variability was due to the diversity within the population, while 55% was due to the genetic differentiation among populations. A total number of 158 bands were detected by ISSR primers, of which 144 (89%) bands with an average of 14.4 bands per primer were polymorphic. The Percentage of Polymorphic Bands (PPB) ranged from 70% (ISSR-7) to 100% (ISSR-1, ISSR-4 and ISSR-5). The average Polymorphic Information Content (PIC), Shannon’s Information index (I), and Number of effective alleles (Ne) were 0.49, 0.28, and 1.09, respectively.