The knowledge about genetic diversity in the wild relatives of wheat provides useful information for breeding programs and gene pool management. In the present study, an assessment of agro-morphological diversity and molecular variability among 70 accessions of Triticum, belonging to T. boeoticum, T. urartu, T. durum and T. aestivum species, collected from different regions of Iran was made. According to phenotypic analysis, all traits except peduncle length, stem diameter and the number of seeds per spike indicated a high level of diversity among studied accessions. Also, principal component analysis identified six components that explained 87.53% of the total variation in agro-morphological traits. In molecular analysis, 15 start codon targeted (SCoT) polymorphism primers produced 166 bands, out of which, 162 (97.59%) were polymorphic. Analysis of molecular variance (AMOVA) indicated the 63% of the variation resided among populations. The maximum value of polymorphism information content (PIC), the observed (Na) and effective (Ne) number of alleles, Nie’s gene diversity (He) and Shannon’s information index (I) was detected for T. boeoticum than the other species. The SCoT-based tree revealed three different groups corresponding to the genomic constitution in Triticum germplasm, which was in part confirmed by STRUCTURE and principal coordinate (PCoA) analyses. Our results indicated a remarkable level of genetic diversity among studied Iranian Triticum species, especially T. boeoticum, which can be of interest for future breeding and other analyses associated with future studies of the wild relatives of wheat. More importantly, our results revealed that SCoT markers could be used to accurate evaluate genetic diversity and phylogenetic relationships among different Triticum species.