The genetic diversity, genetic differentiation and relationship between four short stature cattle populations of south India - Punganur, Iduki, Kasargod and Vatakara - was studied, using 24 microsatellite loci. A total of 164 alleles were observed. The mean number of alleles per locus was 6.58 with mean observed and expected heterozygosity values of 0.70 and 0.75 respectively. The relative magnitude of gene differentiation (FST) was 6% and was significant except between the Iduki and Kasargod populations. The negative FIS values obtained for the majority of loci indicated a lack of population structure in the four populations. Both phylogenetic and correspondence analysis exhibited a closeness between Iduki and Kasargod animals. The results indicated that all four populations were outbred and Kasargod and Iduki animals should be considered as one even though these are reared for different purposes.