The boeoticum (♀) X urartu (♂) F1 hybrids gave small, plump and viable seeds while the reciprocal crosses with T. urartu as the female parent had long, shrivelled and non-viable seeds. Reciprocal nuclear-substitution lines comprising the nucleus of one species into the cytoplasm of the other were developed through repeated backcrossing and were crossed as female parents with respective non-recurrent parents (the cytoplasm donors). The difference between the reciprocal crosses was presumably attributable to different boeoticum urartu genomic ratios in the triploid endosperm rather than to the cytoplasmic difference between the diploid wheats. The endosperm with two doses of the boeoticum and one of the urartu genome resulted in small, plump and viable seed while the endosperm of the reciprocal crosses with two doses of the urartu and one of the boeoticum genome led to large but shrivelled and non-viable seeds irrespective of the cytoplasmic type. One dose of the paternal genome in the triploid endosperm is probably not expressed in the presence of two doses of the maternal genome thereby leading to the difference between the reciprocal crosses. The results reported here indicate that difference between reciprocal crosses may not always be attributed to cytoplasmic difference between the parental species.