Inter Simple Sequence Repeat (ISSR) is a genome region between microsatellite loci. The present study was conducted to study the associations of two ISSR markers with predicted breeding values (PBV) of body weights in sheep. Blood samples were collected from 210 male and female Mehraban sheep, located in 6 flocks in Hamedan province in west of Iran. PCR reactions using (AG)9C and (GA)9C primers produced 28 and 36 fragments (A1 to A28 and G1 to G36), respectively. Moreover, breeding values for birth, 3 month and 9 month body weights of all Mehraban sheep population were predicted by univariate analysis of animal mixed models. Associations of the polymorphic ISSR markers with PBV of the sampled animals were evaluated by general linear model analyses. Four ISSR loci including G14 (790 – 840 bp), G25 (1610 – 1700 bp), A8 (610 – 650 bp) and A26 (2110 – 2200 bp) had significant associations with PBVs of body weight whereas the animals with G14, G25, A8 or A26 bands had a lower PBV of body weight. It seems that the G14, G25, A8 and A26 ISSR loci are likely to contain or linked to some QTLs or major and minor genes affecting body weight and could be used in marker assisted selection programmes
