Molnar, S. J., Charette, M. and Cober, E. R. 2012. Mapping quantitative trait loci for water uptake in a recombinant inbred line population of natto soybean. Can. J. Plant Sci. 92: 257-266. Small-seeded natto soybeans are soaked in the first step of producing natto. Water uptake traits play a role in the quality of the end product. The objectives of the current study were to use a recombinant inbred line (RIL) mapping population contrasting for water uptake traits to develop its molecular marker recombination map, and to use quantitative trait locus (QTL) analysis to characterize the genetics of water uptake and identify molecular markers for marker assisted breeding. A RIL population (AC Colibri×OT91-3) was tested for multiple years at Ottawa, Ontario, Canada. Two water uptake parameters (a16 and b) were estimated by fitting a curve for an exponential rise to a maximum. Both parameters were affected by year, genotype and the interaction effects. Seed yield, seed composition and agronomic traits were also measured. Simple sequence repeat (SSR) markers were used to genotype the population and develop a recombination map. QTL analysis identified two QTL for a16 on molecular linkage groups (MLG) D2 and E and three QTL for b on A2, J and M. Three of these QTL map to similar intervals as known QTL for seed weight, seed yield and seed fill in diverse populations. The fourth may correspond with a known QTL for water absorbability during germination and the fifth maps at or near known flowering time and maturity QTL.