Previous research found that the population density of Heterodera glycines in soybean fields fluctuated during the growth of soybeans. However, the population density in soybean root was unclear. In this study, the dynamics of soybean cyst nematode (SCN; Heterodera glycines, race 4) in soybean roots were investigated over a period of 2 years. Soybean plant roots were sampled during a period of 7-37 days after seedling emergence, and SCN in taproots and lateral root were counted. The results indicated that the total population density of nematodes increased with the growth of soybean roots, showing a sigmoid curve. A comparison of nematode density between taproots and lateral roots showed a decrease in the numbers of nematodes in taproots and an increase in the numbers in lateral roots with increasing age of the plants. There was an overall decrease in nematode numbers with increasing soil depth. Our results show that most of the nematodes were found in roots from 5-15 cm soil depths (2006, 81.3-91.4%; 2007, 86.6-97.6%) during the soybean seedling growth stage, which may provide some useful information for integrated management of soybean cyst nematode.