The development of soybean varieties with reduced polyunsaturated fatty acid contents, mainly linolenic acid, and higher contents of oleic acid is an important goal of soybean breeding programs.  These modifications should lead to an increase on the oxidative stability of the oil fraction and consequently of its shelf life. The objective of this study was to evaluate the genetic distances among soybean cultivars with different fatty acid contents using microsatellite markers and to determine the relationship between the genetic distances and fatty acid content. Seven soybean genotypes (BARC-12, B412113, C2022, CS-303, CS92 6602, N85-2124, N85-2176), from the Soybean Breeding Program for Quality and Flavor (PQMS/BIOAGRO), were utilized in the present work. The DNA was extracted from samples of leaves of each genotype. One hundred microsatellite primer-pairs were used for DNA amplification by the PCR technique. Fifty-seven of the primer-pairs revealed polymorphic bands among the genotypes. Based on this information, pairwise genetic dissimilarities were determined according to the complement of the simple match coefficient. A dendrogram was  built based on the dissimilarity matrix the genetic distances were projected on the bidimensional plane. The Tocher cluster method allowed the formation of four divergent groups: group 1: CS 92 6602, CS303; group 2: BARC-12, N85-2176; group 3: C2022, B412113; group 4: N85-2124. The Pearson correlation coefficient calculated between the genetic distances by microsatellite markers and the Mahalanobis distances based on fatty acid contents was not significant (r = 0.38).  However, the groups obtained through both methods were coincident.