This study is a continuation of our earlier reports on the identification and mapping of the Soybean mosaic virus (SMV) strain SC3 resistance gene present on chromosome 13 (LG F) of soybean (Glycine max (L.) Merr.). We used a combination of fine mapping and transcriptome sequencing to discover the candidate genes for SMV resistance in Qihuang-1. To fine-map the resistance gene, near-isogenic lines (NILs) from a cross between Qihuang-1 (resistant) and Nannong 1138-2 (susceptible) were genotyped with simple sequence repeats (SSR) and insertion and deletion (indel) markers to identify recombination events. Analysis of plants carrying key recombination events placed the resistance gene to a 180-kb region of the ‘Williams 82’ genome sequence with 17 annotated genes. Transcriptome and quantitative real-time PCR (qRT-PCR) analyses revealed that SMV resistance in Qihuang-1 was probably attributable to the four candidate genes (Glyma13g25920, Glyma13g25950, Glyma13g25970 and Glyma13g26000). The four candidate genes identified in this study can be used in further studies to investigate the role of resistance genes in conferring SC3 resistance in Qihuang-1.