Interspecific F₁ hybrids were synthesized between Brassica tournefortii (2n=20, TT) and B. rapa var. yellow sarson (NRCYS-05-02) (2n=20, AA) by sexual mating. The F₁s were obtained only when B. tournefortii was used as the female parent. Morphological, cytological and sequence tagged microsatellite sites (STMS) based molecular analyses were carried out to confirm the hybrid nature of F₁ plants. Morphologically, the F₁ plants were intermediate for most of the morphological attributes. Although, the F₁s showed poor pollen fertility, a few seeds were obtained from open pollination in the surroundings of B. rapa. The F₁ plants showed predominance of univalents (53.66%), a typical feature of wide hybrids. The occurrence of chromosome association ranging from bivalents (0–4), trivalent (0–1) and quadrivalent (0–1) in the F₁s indicated homeologous pairing between the T and A genomes. STMS analysis of the parents and the F₁s revealed a high degree of similarity (75%) and rearrangements in the two genomes during or after their fusion. The study suggests that B. tournefortii has partial genome homeology with B. rapa which could be exploited in crop improvement programmes, particularly breeding for tolerance/resistance to white rust and mustard aphid.