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Phylogenetic relations among 12 wild species of almonds, one cultivated almond and one species of peach were investigated by using of ITS1-5.8S rDNA-ITS2 sequences and trnL region of chloroplast DNA. To do this, maximum-parsimony and neighbor joining analysis adopted. Results of ITS data showed that studied species of Prunus only divided in two groups but incapable to separate different sections. P. tenella showed more diverse genetic distance in compare to other studied species and it seems that this species does not belong to Amygdalus. Also, by using the ITS data it can be reported that Prunus is monophyletic. In this research, the genetic distances for each pair of species were determined and the average genetic distance between species shows only the lowest genetic distance within the genus. Therefore, Prunus is a single genus. Regarding its high similarity of trnL region in wild almond species, it can be reported that maternal ancestor of Prunus is the same and trnL is not optimum marker to separate species of almond.