Although common bean plants can fix atmospheric nitrogen (N2), this process is insufficient to meet the total nitrogen (N) demand of the crop. Thus, the objective of the present study was to compare different N‐responses indices of common bean cultivars in contrasting N fertilization environments. In addition, the genetic variability of the cultivars was verified using SNP and AFLP markers. Cultivars that showed high tolerance to low‐N (LNTI) generally had low N‐agronomic efficiency (NAE), confirming the complexity of simultaneously selecting for genotypes that show both traits. The performance under contrasting N (PCN) index presented the highest heritability and selective accuracy estimates, suggesting PCN may be the most appropriate index to select genotypes. The cultivars were grouped into four groups using molecular markers. Based on the PCN index, cultivars assigned to molecular groups 1 (‘IAC Sintonia’, ‘IPR Bem‐te‐vi’, ‘BRS Notável’, ‘IPR Juriti’, and ‘BRSMG Pioneiro’) and 2 (‘IPR Sabiá’, ‘IPR Quero‐Quero’, and ‘IPR Campos Gerais’) were recommend for future crosses aiming at developing cultivars less dependent on N fertilizers.