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Citrus reticulata Blanco (mandarin orange) is the most commercially cultivated citrus fruit crops in India. North eastern hill region of India is specifically known for its cultivation where the cultivation of citrus is most extensive with great variations. In present study, ISSR markers are used to evaluate the genetic and population structure of 18 populations of mandarin orange cultivated in this region. A total of 146 amplified fragments were generated from 26 primers showing a 53 percent polymorphism of loci. However a pairwise similarity values ranged from 0.93 to 0.98 revealing a very low genetic diversity. This is supported by the low mean values (0.0755 and 0.1410) of heterozygosity (Ht) and Shannon information index (I) respectively. A UPGMA dendrogram separated the 18 populations into two main clusters. Comparative study of the dendrogram, principal co ordinate analysis (PCoA) and structure analysis showed a general agreement between the clustering patterns of the C. reticulata populations. Mantel test showed no correlation between the genetic and geographic distance (r = 0.07, P < 0.140), suggesting that the genetic differentiation is not related to the geographic locations. AMOVA (analysis of molecular variance) revealed a higher genetic differentiation among populations (78%) rather than within the population (22%). The result of this study will be helpful for management and conservation of C. reticulata genotypes found in this region.