The genetic diversity among 3 dwarf breeds of cattle in India, viz. Malnad Gidda, Punganur and Vechur were analysed using 12 sets of microsatellite markers. All 11 amplified microsatellite loci were polymorphic with a mean number of alleles of 7.818±1.66 across breeds and in different breeds it ranged from 7.273 in Malnad Gidda to 3.546 in Vechur. The mean polymorphic information content (PIC) value observed and expected heterozygosity values across the population were 0.642, 0.610 and 0.683, respectively. A moderate level of inbreeding was observed with the inbreeding estimates ranging from -0.027 (ILSTS6) to 0.271 (HAUT24). Among the 3 breeds the highest mean number of alleles (7.273), mean PIC value (0.639), observed heterozygosity (0.630) and lower inbreeding estimates at majority of loci were observed in Malnad Gidda cattle indicating high degree of heterozygosity compared to Punganur and Vechur breeds. Even though departure from Hardy Weinberg Equilibrium (HWE) was found in Vechur and Punganur cattle population at majority of the loci, the population combining the 3 breeds was maintained at HWE with respect to most of loci under study. The genetic distance analysis revealed highest genetic distance between Vechur and Punganur (0.331) and lowest between Malnad Gidda and Punganur (0.125)
