Abstarct: Abstract: Barberry with high resistance sharbs which can grown in adverse weather conditions for other fruit trees and it is a suitable crop for cultivation in Iran, especially in South Khorasan province. In a research, a series of interspecies crosses between seedless barberry and selected genotypes of wild type barberries was done in 2010. Finally, 90 shrubs have fruit bearing on the barberry collection in the Faculty of Agriculture of Shahrood University of Technology. The aim of this study was to investigate the genetic and morphological diversity and fingerprinting of barberry inter-species hybrids using morphological, phytochemical and phenological traits and ISSR and RAPD markers, In this study, using 81 morphological and phytochemical traits and 5 phenological traits in 90 interspecies hybrid genotypes of barberry and seedless barberry were evaluated and in the molecular section using 10 RAPD marker primers and 9 ISSR marker primers was used in 29 selected genotypes of collection, 3 parent genotypes, ornamental barberry and seedless barberry. The most important morphological and phytochemical traits can be the maximum length, width, berry and cluster, seedless and low of seed in genotypes, number of berries per cluster, number of clusters in the last 1.3 of the cluster, fruit flavor, weight Wet and dry fruit, fruit yield, fruit juice, anthocyanin, antioxidant, vitamin C, total soluble solids and titratable acidity were used. Among the best genotypes that were evaluated using these traits, genotypes include 0516, 0608, 0611, 0524, 0404, 0536, 0519, 0525, 0528, 0703, 0530, 0103, 0515, 0528, 0203, 0603 , 0607 and 0601, of which genotypes 0202 and 0205 are completely seedless and, also, one of the most important genotypes of forage seeds, which has important characteristics, including genotype 0402 with the highest volume of fruit and antioxidant, 0507 with the highest amount of juice, total phenol contents and cluster weight, 0201 with the lowest pH and ta, 0403 with the highest amount of soluble solids, 0408 with the highest berry length, 0503 with the highest fruit fresh weight and berry width, 0401 with the highest fruit dry weight, 0501 with the highest weight yield in 1398, 0508 with the highest anthocyanin content 98 bands were created from 34 ISSR primers in 34 genotypes. The highest number of bands and resolution was observed in the UBC-890 primer with 14 bands. The coefficient of dissimilarity between genotypes ranged from 0.23 to 0.86. Dendrograms of clusters of genetic diversity in ISSR marker 34 barbe-rry genotypes were identified and grouped in RAPD primers in 34 genotypes of 112 bands. The highest number of bands was observed in OPN-13 and OPM-16 primers with 13 bands and the highest resolution was observed in OPM-16 and BD-13 primers. The dissimilarity coefficient between genotypes ranged from 0.21 to 0.85. Clusters of genetic diversity in ISSR marker in 34 Barberry genotypes were identified and grouped into four groups. According to the obtained results, genotypes 0609 and 0515 have more genetic distance than other genotypes. .