In many genera, of both plants and animals, divergence and speciation is often accompanied by massive changes in the amount of nuclear DNA. These changes, in turn, result from amplification or repetition of base sequences within the chromosomal DNA. The chromosomes of different species are consequently of different size and structure. Observations in hybrids between species differing in nuclear DNA amount show that, despite large differences in DNA content, homoeologous chromosomes pair effectively at pachytene and form chiasmata. Only when the DNA differences are very large, of the order of 60% or more, is pairing at pachytene and chiasma formation impaired. The conclusion is that large scale chromosome structural change due to the repetition of DNA base sequences has surprisingly little effect upon the homology of chromosomes, i.e. their ability to pair effectively and form chiasmata at meiosis. Similar repetitive sequences are frequently distributed widely among non-homologous chromosomes within complements. The question then arises as to what prevents chiasma formation between the non-homologous chromosomes which have in common DNA segments of similar sequences? Evidence is presented which indicates that prevention is under the control of the genotype. The control is effected in one of two ways, either by the suppression of pairing at zygotene or pachytene or by suppression of chiasma formation subsequent to pairing.