Genetic diversity is an essential factor for the success of any plant breeding program and should be considered to ensure genetic gain through breeding. In Brazil, research on the genetic diversity and population structure of soybean is required since the species is an important commodity of the country. The study addressed the genetic diversity and population structure of 77 soybean genotypes using 35 SSR markers. The estimate of the diversity index showed that the level of genetic diversity in the soybean collection is low. Similarly, the Jaccard coefficient and Bayesian model based on clustering analysis confirmed the low diversity among soybean genotypes, providing evidence for the assumption of a genetic bottleneck effect on Brazilian soybean genotypes. The results also reinforced the importance of finding and incorporating new genetic resources of soybean in the genetic pool of Brazilian soybean to warrant genetic gain in soybean breeding in the future.