Breeding soybeans for multiple and durable resistance is most practical and economic in protecting yields. Identification and use of specific genes and molecular markers would greatly improve the breeding efficiency towards disease resistance. In this study, a total of 1885 disease resistance gene analogs (RAG) distributed on 20 whole soybean genomes were analyzed. In this molecular analysis, genetic positions of RGAs were calculated; 20 genetic maps with the 1885 RGAs were structured, and all RGAs were also merged into the public soybean consensus maps. RGAs as candidate genes/QTLs and associated SNP markers were postulated to be located at the regions for many resistance loci, including Rag1 and Rag2 for aphid (Aphis glycines) tolerance; Rcs3 for resistance to frogeye leaf spot (Cercospora sojina); rhg1, Rhg4, Rhg5, qtlB1, qtlD2, qtlE, and qtlO for soybean cyst nematode (Heterodera glycines) resistance; Rps1, Rps3/8, and Rps2/6 for Phytophthora root rot (Phytophthora sojae) resistance; Rpg1 for resistance to bacterial blight (Pseudomonas syringae pv. glycinea); Rpp1, Rpp2, and Rpp(Hyuuga) for Asian rust (Phakopsora spp.) resistance; Rsv1, Rsv3, and Rsv4 for Soybean Mosaic Virus (SMV) resistance; a gene on Chr. 16 (LG J) for resistance to powdery mildew (Microspaera diffusa); a gene on Chr. 17 (LG D2) for resistance to bacterial leaf pustule (Xanthomonas axonopodis pv. glycines); and a QTL on Chr. 18 (LG G) for purple seed stain and leaf blight (Cercospora kikuchii) resistance, and a QTL on Chr. 10 (LG O) for resistance to root-knot nematodes (Meloidogyne spp.) in soybean. The SNP markers derived from RGAs can be used in molecular breeding as a tool of marker-assisted selection for disease resistance in soybean breeding programs.