Plastid markers are typically highly conserved, making them especially valuable for revealing phylogenetic relationship at or above the species level. Thirty five accessions of Cucumis melo L., belonging to the groups Flexuosus, Cantalupensis, Inodorus and Dudaim collected from western-north to western-south part of Iran analyzed was used for plastid single nucleotide polymorphism. A pair of dCAPS primer was used to estimate different nucleotide type of plastid subtype sequences. PCR amplification of the plastid DNA fragment containing rpl16 and rpl14 sequences was performed and products were digested with Apo? in 50°C thermal condition for 2 h. After digesting products subjected to electrophoresis on 2.5% agarose gel. Single nucleotide polymorphism of 35 accessions from various groups were detected by different size of band on gel and polymorphism at two loci were determined as A and T types. Results showed that all Flexuosus and Inodorus accessions revealed T-type plastid identity in loci. Two accessions of the Dudaim group and one accession of the Cantalupensis group classified in A-type group. Based on this investigation there was chloroplast genome variation between different types of melons in Iran and also plastid type distributed allopathically.