This report focus on EST-SSR based evaluation of genetic diversity in salt tolerant plant from six species in Chenopodiaceae. Thirty-one pairs of EST-SSR primers were designed according to ESTs sequence collected from Salicornia and Suaeda genera. Only sixteen out of all primer pairs successfully amplified the DNA fragments by using PCR procedure across all samples, which demonstrated a 51.6% over all primers was transferrable. Total 18 polymorphic loci were detected by the 16 primer pairs, and allele number at each locus ranged from 2 to 4, indicating a wide range of genetic diversity. Clusterring analysis based on Nei’s genetic distance showed that the six plants could be grouped into three clades, and the division was confirmed by principal component analysis. More over, this grouping profile was mainly attributed to polymorphism of three ESTs, e.g. DY529957, DY529903 and DY529885. According to the sequence similarity, the three ESTs were assumed to encode an auxin-repressed protein (ARP), Defensins (Def) and hypothetical proteins, respectively, Both ARP and Def were well documented to be involved in salt stress responds but form different pathways in plants. This result implies that different mechanism might be evolved among the genera.