The invention relates to methods and compositions for identifying soybean plants that are tolerant, have improved tolerance or are susceptible to Phytophthora root rot infection. The methods use molecular genetic markers to identify, select and/or construct disease-tolerant plants or identify and counter-select disease-susceptible plants. Soybean plants that display tolerance or improved tolerance to Phytophthora root rot infection that are generated by the methods of the invention are also a feature of the invention.