Salsola is one of the largest genera in the tribe Salsoleae within Amaranthaceae, with many species that share morphological characteristics, which makes it a challenging genus to study. In this study, 11 quantitative and eight qualitative morphological traits were evaluated and measured. Ward’s dendrogram showed two main clusters: one composed of S. brachiata and S. turcomanica, and the other composed of two subclusters, with populations of S. kali, S. incanescens, S. orientalis and S. dendroides. In addition, we performed molecular phylogenetic analyses conducted with sequence data from nrDNA (ITS and ETS) and cpDNA markers (psbB-psbH and atpB-rbcL) under maximum parsimony, Bayesian inference and maximum likelihood approaches. All the members were clustered into a well-supported clade (PP = 1, ML/BS = 0.89) composed of two subclades: subclade A included S. turcomanica and S. brachiata (PP = 0.90, ML/BS = 73) and subclade B (PP = 0.95, ML/BS = 81) comprised S. incanescens, S. orientalis, S. dendroides and S. kali. The current study provides novel insights at morphological and molecular levels, as well as the results of molecular studies based on nr- and cpDNA sequence data that are congruent with morphological analyses.