Flowers of an alloplasmic male-sterile tobacco line, comprised of the nuclear genome of Nicotiana tabacum and the cytoplasm of Nicotiana repanda, develop short, poorly-pigmented petals and abnormal sterile stamens that often are fused with the carpel wall. The development of flower organ primordia and establishment of boundaries between the different zones in the floral meristem were investigated by performing expression analysis of the tobacco orthologs of the organ identity genes GLO, AG and DEF. These studies support the conclusion that boundary formation was impaired between the organs produced in whorls 3 and 4 resulting in partial fusions between anthers and carpels. According to the investigations cell divisions and floral meristem size in the alloplasmic line were drastically reduced in comparison with the male-fertile tobacco line. The reduction in cell divisions leads to a discrepancy between cell number and cell determination at the stage when petal and stamen primordia should be initiated. At the same stage expression of the homeotic genes was delayed in comparison with the male-fertile line. However, the abnormal organ development was not due to a failure in the spatial expression of the organ identity genes. Instead the aberrant development in the floral organs of whorls 2, 3 and 4 appears to be caused by deficient floral meristem development at an earlier stage. Furthermore, defects in cell proliferation in the floral meristem of the alloplasmic male-sterile line correlates with presence of morphologically modified mitochondria. The putative causes of reduced cell number in the floral meristem and the consequences for floral development are discussed.