This study compare the effect of the slope direction of genetic variation and morphological diversity of male and female Juniperus polycarpos and effect of slope position of genetic variation in Juniperus polycarpos in Chahar Bagh habitat. For this study, samples of branches and scales were done two years of growth. Immediately, the samples were prepared extracts. Quantitative and qualitative studies of the peroxidase activity were measured using a spectrophotometer, poly acrylamide gel electrophoresis (PAGE) and morphological evaluation was performed using Binoculars. The results showed that, compared the branch and scale, scales has more variety.The results showed that, compared organs scales with branches,scale has a greater variety of branch. The results morphological marker are also accordance with isozyme markers. But the diversity of isozyme markers showed more morphological markers.Eastern slopes and back slopes and male trees were more diverse.