The transcription factors FLOWERING LOCUS C(FLC) and SHORT VEGETATIVE PHASE(SVP) can interact to form homologous and heterologous protein complexes that regulate flowering time in Brassica juncea Coss.(Mustard). Previous studies showed that protein interactions were mediated by the K domain,which contains the subdomains K1,K2 and K3. However,it remains unknown how the subdomains mediate the interactions between FLC and SVP. In the present study,we constructed several mutants of subdomains K1–K3 and investigated the mechanisms involved in the heterologous interaction of BjFLC/BjSVP and in the homologous interaction of BjFLC/Bj FLC or BjSVP/BjSVP. Yeast two-hybrid and β-galactosidase activity assays showed that the 19 amino acids of the K1 subdomain in BjSVP and the 17 amino acids of the K1 subdomain in BjFLC were functional subdomains that interact with each other to mediate hetero-dimerization. The heterologous interaction was enhanced by the K2 subdomain of BjSVP protein,but weakened by its interhelical domain L2. The heterologous interaction was also enhanced by the K2 subdomain of BjFLC protein,but weakened by its K3 subdomain. The homologous interaction of BjSVP was mediated by the full K-domain. However,the homologous interaction of BjFLC was regulated only by its K1 and weakened by its K2 and K3 subdomains. The results provided new insights into the interactions between FLC and SVP,which will be valuable for further studies on the molecular regulation mechanisms of the regulation of flowering time in B. juncea and other Brassicaceae.