Interclass hybridization between soft and hard wheat (Triticum aestivum L.) results in new genetic combinations of potential value. We investigated whether interclass hybridization could improve end-use quality of both classes. Our objectives were to analyze quality traits in a population of recombinant inbred lines (RILs) derived from a cross between the good quality soft white wheat NY6432-18 (NY18), and good quality hard white wheat Clark's Cream (CC), identify quantitative trait loci (QTLs) for those traits, and use linkage analysis to determine which parent was contributing favorable alleles at specific QTLs for a given trait. The population was assessed for milling, protein and dough mixing, hydration, cookie and loaf traits. Traits were measured in two to six environments grown over three seasons in Ithaca, NY. The molecular map for the population contains 370 molecular markers including restiction fragment length polymorphisms (RFLPs), microsatellites, and markers derived from known function genes in wheat. Linkage groups have been located to all the wheat chromosomes except for 7D. Pinb derived from the puroindoline b gene on chromosome 5DS was the major QTL for milling, hydration, and cookie baking traits. The major QTL for mixograph peak time was at the Glu-Dy1 marker, derived from Glu-D1-2 gene on chromosome 1DL. The Glu-Ax1 and Glu-By1 markers were QTLs for mixograph peak height and tolerance, respectively. QTLs for flour protein quantity were detected on chromosome 2B. With the exception of the hydration traits, multiple regression models included alleles from both parents. Interclass hybridization may be an underexploited wheat breeding strategy for improvement of agronomic and quality traits in wheat.