Soybean (Glycine max L.) is an annual, self-pollinated species, whose genetic base in Brazil is the result of several cycles of selection and effective recombination among a relatively small number of genotypes selected from the USA cultivars. This frequent selection, admixed population, and the crossing of a small number of cultivars can lead to increase the genetic relationship and affect the patterns of population structure. These factors affect the patterns of linkage disequilibrium (LD) blocks, which can be an effective approach for the screening of target loci for agricultural traits in cultivars of tropical soybean. The objectives of this research were to analyze LD blocks, estimate population structure and relatedness through of genotyping of 169 cultivars of tropical soybean by using a BARCSoySNP6K of Illumina iScan platform. The genotyping revealed a high genetic relatedness and population structure among the cultivars of soybean in Brazil, suggesting the existence of a shared genetic base. Our results provide a help to understand the distribution of genetic variation contained within the Brazilian soybean cultivar collection. We showed that the extensive use of a small number of elite genotypes in Brazilian breeding program further reduced the genetic variability, generate extensive LD and probably increase the haplotype block size. These results are in agreement with results of USDA soybean collection, mainly with accessions of north American, when compared with wild and landraces accessions. We constructed a small haplotype block maps (941 blocks), which may be useful for association studies aimed at the identification of genes controlling traits of economic importance in soybean.