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Plant morphology and cytogenetics of progenies from intergeneric hybrids between Brassica juncea and Orychophragmus violaceus were studied. The progenies comprised three F3 populations derived from three mixoploid F2 plants with different morphology and chromosome numbers. The following results were obtained. (1) The differences in plant morphology were maintained among the three F3 populations. (2) All F3 plants were mixoploids, mainly composed of cells with serial chromosome numbers in certain ranges. In plants with similar serial numbers, the cells with the highest three chromosome numbers accounted for 66–89% of the total cells. (3) In mitotic metaphase spreads, it was possible to differentiate some large and more darkly stained chromosomes which showed a later chromatid separation than the others. Lagging chromosomes and micronuclei were often observed in anther‐wall cells. (4) In pollen mother cells (PMCs) at diakinesis and metaphase I, some large and more darkly stained bivalents and univalents were easily distinguished, and the chromosomes composing these bivalents segregated later than the others. Various segregation patterns were observed at anaphase I. At both anaphase/telophase I and II, some large and darkly stained chromosomes lagged between or were included in polar groups or daughter nuclei. (5) The differentiable large and darkly stained chromosomes in mitotic and meiotic cells were conceived as of O. violaceus origin. Differences in timing between the parental chromosomes during mitotic and meiotic divisions very likely contribute to the complete and partial separation of parental genomes proposed to occur in the B. juncea×O. violaceus hybrids.