In the past decade, there has been a remarkable revolution in the field of molecular genetics. This revolution has been founded on many experimental observations that indicate that the DNA sequence alone does not carry all of the information required to determine the phenotype of the organism. It has long been known that there are many awkward exceptions to ‘normal’ Mendelian genetics that have defied explanation by conventional theory, for instance, paramutation that was first identified in the 1950s. Now, these have been joined by the discovery of new phenomena of the same non-Mendelian nature, most significantly ‘transgene silencing’ in plants where new DNA sequences have been added to the genome. These observations challenged what was the contemporary view of the phenotype as a system dictated entirely, and in a linear fashion, by the sequence of DNA nucleotides coding for proteins. The intensive efforts to determine why these apparent ‘exceptions’ to Mendelian rules exist, and to discover the molecular mechanics and rules of behaviour governing these non-Mendelian phenomena, has generated a profoundly important and exciting set of data. This review intends to briefly and simply introduce and review this new field, named ‘epigenetics’ (i.e. ‘upon genetics’), in plants for the benefit of an audience unfamiliar with such developments, although we are profoundly aware that substantial and detailed reviews on this subject are now ubiquitous. These will be referenced throughout the review; indeed, a particularly interesting and relevant introduction to the history and changing concept of epigenetics can be found in Jablonka and Lamb (2002). However, the main thrust of this two-part review is to address a hitherto little explored ramification of these discoveries, i.e. the relationship of epigenetics to the evolution, morphology and taxonomy of plants. We believe this new field of epigenetics will be an ‘epiphany’ in these conventional fields of botany when its exceptional significance becomes known more widely.