Low-molecular-weight glutenin subunits (LMW-GS) are a component of the gluten network and play a key role in determining the viscoelastic properties of wheat dough. Aegilops species have been shown to be an important source of variation for valuable traits for wheat breeding. However, very little is known about LMW-GS genes in section Sitopsis species, which are closely related to the B genome of common wheat. Ten accessions of Sitopsis species were evaluated for variability of LMW-GS genes, and 20 novel genes were obtained, of which nine were LMW-m and 11 were LMW-s genes. Only two were pseudogenes, corresponding to one LMW-m and one LMW-s gene. Six groups of genes were detected: three for each of the LMW-m and LMW-s genes. All groups of LMW-s genes and one of LMW-m genes (pGluU) detected were not related to B-genome genes from common wheat, whereas the remaining genes were. The single-nucleotide polymorphisms, and insertions and deletions, detected in active variants compared with those from common wheat could affect structure protein. The analysis of reactive epitopes for coeliac disease revealed that LMW-s subunits lacked toxicity, as did the pGluU LMW-m subunits; the other LMW-m subunits were less toxic than that from common wheat.