Branched spike or supernumerary spikelet (SS) is a naturally occurring variant in wheat and holds great potential for increasing the number of grains per spike, and ultimately, increasing wheat yield. However, detailed knowledge of the molecular basis of spike branching in common wheat is lacking. In the present study, a recombinant inbred line (RIL) population derived from the cross of an SS accession and an elite non-SS line was developed and evaluated over four to six environments for seven SS-related traits to identify the genetic basis of SS in wheat. A framework linkage map was generated using 939 diversity arrays technology (DArT) markers. Composite interval mapping (CIM) identified a total of seven consistent quantitative trait loci (QTL) located on five chromosomes (2D, 5B, 6A, 6B, and 7B), suggesting a polygenic inheritance of SS. The phenotypic variation explained (PVE) by individual QTL ranged from 3.3 to 37.3%. The QTL located on 2D (QSS.ndsu-2D) and 7B (QSS.ndsu-7B.2) have major effects (PVE > 15%), while the remaining five QTL (QSS.ndsu-5B, QSS. ndsu-6A, QSS.ndsu-6B.1, QSS.ndsu-6B.2, QSS.ndsu-7B.1) have minor effects (PVE <15%). Comparison of the genomic locations of the QTL suggested that QSS.ndsu-2D was located in the same regions on 2DS, where QTL for several traits have been reported. However, the remaining six QTL for SS are reported for the first time. Multiple interval mapping (MIM) showed that all seven QTL are involved in epistatic interaction. The major genomic regions controlling these SS-related traits may prove invaluable for wheat improvement and could also be the target for future studies aimed at cloning these genes.