ABSTRACT The cultivation of second-harvest with soybean crop after first-harvest with maize crop has become an alternative to aggregate income to farmers in the South region of Brazil. However, there is little information about this cropping system in this region. The aims of this study were to: (i) evaluate the agronomic performance of soybean (Glycine max L.) cultivars growing in second-harvest during the summer; and (ii) evaluate the genetic divergence of the cultivars based on qualitative and quantitative traits. To do this, 18 soybean cultivars were evaluated in three field trials, sown during January in the northwestern region of Rio Grande do Sul state, Brazil. In each experiment, a randomized block design with four replicates was used. Five quantitative traits (representing the agronomic performance of the cultivars) and 12 qualitative traits (morphological descriptors) were assessed aiming at studying the genetic divergence. Variance components and genetic parameters were estimated using mixed models and BLUPs for genotypes were estimated for each quantitative trait. The cultivars FPS Iguaçu RR and BMX Turbo RR have good agronomic performance and are, based on quantitative and qualitative traits, genetically distant. These cultivars have shown agronomic features that allow their cultivation in the second-harvest in the northwestern of Rio Grande do Sul in addition to be potential genitors for future soybean breeding programs.