Quantitative trait loci (QTL) mapping is a powerful tool for characterization of the genetic basis of complex traits. Very often, more than two populations are studied for the same traits. Objectives of this study were to: (1) extend least squares interval mapping (LSIM) for pooled analysis on data from multiple populations and (2) analyze pooled data from two soybean mapping populations for resistance to SCN in soybean. LSIM was extended for pooled analysis on data from multiple populations by inclusion of populations and cofactor markers as indicator variables and covariate variables separately in the multiple models. The pooled analysis on data from two soybean populations, Hamilton x PI 90763 and Magellan x PI 404198A, was conducted for resistance to soybean cyst nematode races 2 and 5. Where a QTL was shared among populations, the pooled analysis showed increased LOD values and therefore it may have an advantage over separate analyses. Where a QTL was not shared among populations, however, the pooled analysis showed decreased LOD values and therefore it may have no advantage over separate analyses. The pooled analysis played a unique role in examining the difference of a QTL among different mapping populations.