Soybean has become one of the most important crops to the United States, resulting in a need to improve its disease resistance. The objectives of this study were to 1) design primers and develop PCR-based markers from disease-related expressed sequence tags (ESTs) and resistance gene analogues (RGAs), 2) assess the utility of such markers by diversity analysis of 12 soybean parental lines, and 3) search for possible association of the markers with known disease resistance genes by constructing a linkage map. The diversity analysis will allow this study to determine how well each marker can distinguish genotypes in soybean. Identifying the location of our markers in the soybean genome with the linkage map, will allow those related to disease resistance to be selected. A total of 202 simple sequence length polymorphism (SSLP) markers were constructed using a set of 1218 disease-related ESTs. Furthermore, 22 markers were constructed using previously identified RGA sequences. Both sets of markers were able to detect polymorphism in the diversity analysis. Also, 48 of the SSLPs, five of the RGAs, and 150 molecular markers were used to construct a soybean linkage map using 114 recombinant inbred lines (RILs). Several markers mapped to chromosomal regions known to contain disease resistance genes. This study has created a framework map, which will be useful for identifying the location of resistance genes, marker-assisted selection for resistance, discovering novel resistance genes, and understanding genome organization of resistance pathways in soybean. An effective approach to develop "candidate gene" markers has been demonstrated. / Master of Science