Modern wheat (Triticum aestivum L.) cultivars are characterized by having spikes with fusiform architecture and rachis nodes with one spikelet. However, genotypes with supernumerary spikelets (SS) in which rachis nodes have more than one spikelet exist in nature. Although this may be a promising trait that increases yield components, detailed knowledge about the molecular basis of SS trait and their influence on other wheat traits is still lacking. In the present study, a population of 163 recombinant inbred lines (RILs) derived from an elite line and an exotic line with SS was used to identify QTL for SS and other wheat traits. The RILs, seven checks and the two parents were evaluated for seven SS-related, 10 spike-related, 10 agronomic, and eight quality traits over four to six environments in North Dakota. A genetic map of 3,114.2 cM of length with an average distance of 4.6 cM between any two marker loci was developed using 159 RIL and 939 DArT markers. Composite interval mapping identified 221 QTL, out of which 29% were consistent QTL and 19% were major QTL. Most of the QTL were located on the B-genome (44%) followed by the A-genome (37%) and D-genome (19%). The exotic parent with SS contributed 48% of alleles that increased phenotypic values of the traits suggesting the possibility of enriching the breeding germplasm with genes from this genotype. Seven consistent QTL with epistatic interaction were associated to the SS. QSS.ndsu-2D, a major QTL for SS, was co-located in a cluster of QTL on 2DS demonstrating either pleiotropic effect or closely linkage with 19 QTL for other wheat traits. Similarly, a major QTL associated with glume pubescences (QPP.ndsu-1A.1) was co-located on 1AS with seven QTL for other wheat traits. Major and consistent QTL are targets for further marker assisted selection in wheat breeding programs and/or for research projects aiming of gene cloning.