This study was carried out in order to verify whether natural selection acts on segregating common bean populations grown in the presence and absence of N, and to verify that natural selection affects the frequency of microsatellite alleles specifically, and in order to identify those that can assist in selection. Four populations from the crosses Ouro Negro x CI-107 and VC-5 x IAPAR-81 were carried forward in bulk to F8 at both levels of N. Ouro Negro and VC-5 are considered stress tolerant to nitrogen and IAPAR-81 and CI-107 responsive. One hundred progenies were obtained from each cross and grown in the presence and absence of N. DNA was extracted from 400 progenies, of which 194 were evaluated in the rainy season and 79 in the winter crop for grain yield. These progenies were evaluated in two separate experiments with and without N, in a 14 x 14 lattice design during rainy season and 9 x 9 in the winter season. We selected 35 pairs of polymorphic primers from the parents, with 20 being common from the two crosses. Using DNA of the 400 progenies, it was found that natural selection acted in 33 loci, in at least one environment and cross, and that alleles of the four parents were favoured by natural selection. QTLs were identified for the response rate of N and for grain yield and the linked markers are potential for assisted selection, especially the two most stable; BMD-20, in response to the use of N and PVBR-93 for grain yield.