The root‐knot nematode (RKN) species Meloidogyne javanica(MJ) causes substantial root damage and yield loss in susceptible soybean [Glycine max(L.) Merr.] cultivars. In this study, a genome wide association study (GWAS) was undertaken to identify genomic regions controlling RKN resistance in a soybean association‐mapping panel, using single nucleotide polymorphism (SNP) markers and haplotype information. This study was carried out with a sample (n= 124) from the Coodetec soybean gene bank, including some commercial Brazilian varieties. For the phenotypic evaluations MJ inoculum was obtained from roots of cultivar CD 206, a highly susceptible soybean used to maintain MJ for studies at Coodetec. The cultivars CD 208 and BRS CONQUISTA were used as resistant checks while CD 206, R7, and Nidera NA 5909 RG were used as susceptible checks and all 124 lines were genotyped with 6,000 SNP markers. MJ resistance determinants in the soybean panel were linked to SNPs with significant effects, with nine SNPs distributed along chromosomes 7, 13, and 20. The observed average MJ resistance in the group of soybean entries with haplotype GCT, ACC, ACT, and GCC in the markers Gm20_44446670_G_A, Gm13_29739984_C_A and Gm07_8166605_T_C, respectively, represents moderately resistant genotypes. Gm13_29739984_C_A and Gm07_8166605_T_C discriminated resistant and susceptible cultivars better than the marker Gm20_44446670_G_A. These results are particularly promising for soybean‐breeding programs, by not only identifying new resistance‐associated haplotypes, but also suggesting new genetic mechanisms in RKN‐resistance sources.