The Gyr cattle breed (Bos indicus) has become an important breed for milk production throughout the tropical areas. This study investigated the genetic diversity and the relationship between genetic distance and geographic distance. In total, 588 Gyr cows of seven herds from different geographical locations of two states in Brazil were genotyped for 45797 single nucleotide polymorphism (SNP) markers and a subset of 9176 SNP were used to assess genetic diversity. The overall expected heterozygosity of total population was 0.264 0.158, and there was no significant difference between herds. The average of genetic differentiation among all herds measured as FST value was 0.050 0.041. FIT value for the whole population was 0.019 0.058 while the FIS value for the whole population was -0.031 0.047, showing an excess of heterozygotes. Genome wide level of inbreeding based on proportions of the genome being in runs of homozygosity was 0.0537. The assessment of the effective number of migrants by generation (Nm) was 3.49. The largest geographic distance between subpopulations in this study was between Herd_265 and Herd_551 with a spatial distance of 532 km. Both FST and Nei's genetic distance were also greatest between Herd_265 and Herd_551 with values of 0.077 and 0.022 respectively. In the principle component analysis (PCA), the first principle componentaccounted for 4.895% of the total variance and the second principle component condensed 2.526% of the variation. The application of Rousset's isolation by distance method provided a linear relationship between genetic distance and geographical distance: F_ST/(1-F_ST )=-0.035+0.014 ln(d); with 29.89% of the variance explained by this model. The Mantel test, comparing matrices of geographical and genetic distances indicated a positive correlation between those two types of distance, with a trend toward significance (r=0.624, P=0.068).