Recent studies have revealed unexpected high levels of genetic variation across maize inbred lines, which led to violation of colinearity that holds even between species of the grass family. Although activity of certain mobile elements is likely a contributing factor for this kind of intra-specific variations in maize, it is conceivable that other mechanisms might be involved. Here, we report that de novo genetic variation occurred instantaneously in a pair of reciprocal maize F(1) hybrids between inbred lines JAU8 and JAUM. Because expected genetic stability was observed in two other pairs of reciprocal hybrids in which each of these two lines was used as a crossing parent, we consider that the genomic instability in the JAU8/JAUM hybrids is due to specific incompatibilities between the two lines upon hybridization. Pairwise sequence analysis revealed the nature of the genetic changes as predominantly nucleotide substitutions with occasional small indels. At least some of the hybridization-induced genetic variations are likely associated with alteration in cytosine methylation. Given that a substantial portion of the variant bands bear meaningful homology to known or predicted genes, we suspect that the genetic changes and associated epigenetic alterations may have functional consequences.