The Kermani sheep is an important meat producing animal in Iran and its economic efficiency is mainly dependent on its growth and reproduction ability. Inter Simple Sequence Repeat (ISSR) is the genome region between microsatellite loci. The aim of this study was to evaluate the association of two different ISSR markers with predicted breeding values (PBV) of body weight trait in Kermani sheep. Blood samples were obtained from 240 Kermani sheep. Polymerase chain reaction (PCR) was performed using two ISSR primers (GA)9C and (AG)9C. The amplified PCR fragment sizes ranged from 100 to 3100 bp and primers amplified 28 (A1 to A28) and 36 (G1 to G36) fragments, respectively. In addition, breeding values for birth weight, weaning weight (at 3 months of age) and body weight at 9 months of age for all Kermani sheep were predicted by univariate analysis of the animal mixed model. Associations of the loci with predicted breeding values of body weights were evaluated using a general linear model. Five polymorphic ISSR loci, G14, G25, A8, A20 and A26 had significant associations with PBVs of body weight (P<0.05), whereas the animals with presence of the bands significantly had a lower PBV of body weight. It seems that the G14, G25, A8, A20 and A26 ISSR loci may involve or linked to some QTLs or major and minor genes affecting body weight of lambs and therefore, could be used as genetic markers in MAS. © 2016, Iranian Neurogenetics Society. All rights reserved.