Accurate identification of breeding material is very important for the plant breeder. In South Africa, high molecular weight glutenin subunits (HMW-GS) have so far been used for wheat cultivar identification. This method can often not distinguish between cultivars, and other techniques need to be investigated. The aim of this study was to compare HMW-GS, low molecular weight glutenin subunits (LMW-GS) and random amplified polymorphic DNA (RAPDs) for wheat cultivar identification. Five commercial wheat cultivars were analysed using the above three methods. The HMW-GS failed to distinguish between the five cultivars. LMW-GS could clearly distinguish between the cultivars, but banding pattern interpretation was more complicated than for HMW-GS. RAPDs could distinguish between the five cultivars with three different primers, but were expensive and would need an increased number of primers with an increase in cultivars. We concluded that HMW-GS should be used for initial cultivar identification, as it is simple and reliable. Where they fail to distinguish between cultivars, the LMW-GS should be used for final identification.