Malin sheep is the indigenous sheep breed of Malaysia and mainlykept for meat production. A total of 48 individuals from the National Institute of Veterinary Biodiversity (NIVB) in Jerantut,Pahang were used. The objective of this study was to assess the genetic diversity in the Malin using microsatellite markers.Eleven microsatellite loci were successfully amplified in 48 Malin sheep. All loci were polymorphic. A total of 66 alleles were detected. The number of observed alleles per locus varied from 12 to 21, with mean observed number alleles per locus of15.18±4.58. The observed heterozygosity and expected heterozygosity were 0.0189±0.01 and 0.8989±0.01, respectively. The mean polymorphic information content (PIC) value was 0.8970±0.01, indicating that the used markers were highly informative and could be used in parentage identification. Tests of genotype frequencies for deviation from the Hardy-Weinberg equilibrium (HWE), at each locus revealed depature from HWE due to loss in heterozygotes by high levels of inbreeding. The average inbreeding value for the 11 markers investigated was0.9797±0.01 indicating a more homozygous nature of the population. This is the first report of microsatelitte based variations in Malin sheep breed and can be useful for development of a rational breeding strategy for genetic improvement of sheepin Malaysia which may benefit future conservation programmes.