A growing body of evidence suggests that alterations in transcriptional regulation of genes involved in modulating development are an important part of phenotypic evolution, and this can be documented among species and within populations. While the effects of differential transcriptional regulation in organismal development have been preferentially studied in animal systems, this phenomenon has also been addressed in plants. In this review, we summarize evidence for cis-regulatory mutations, trans-regulatory changes and epigenetic modifications as molecular events underlying important phenotypic alterations, and thus shaping the evolution of plant development. We postulate that a mechanistic understanding of why such molecular alterations have a key role in development, morphology and evolution will have to rely on dynamic models of complex regulatory networks that consider the concerted action of genetic and nongenetic components, and that also incorporate the restrictions underlying the genotype to phenotype mapping process. Developmental Dynamics 244:1074-1095, 2015. V C 2015 Wiley Periodicals, Inc.Key words: phenotypic evolution; gene regulation; epigenetics; evo-devo; gene regulatory networks IntroductionIn this review article, we will provide evidence to connect natural phenotypic variation in plants to heritable changes in epigenetic and transcriptional regulation and discuss how plant phenotypic alteration can be explained by the relative position of regulators within gene regulatory networks. In the first section of the article, we show how plant phenotypic variation can be generated by different mechanisms of gene transcriptional regulation. The second section comprises diverse evidence for plant phenotypic evolution related to three main regulatory alterations: epigenetic modifications, cis-regulatory changes, and trans-regulatory changes. We also briefly talk about the fitness costs of natural regulatory variation in plant populations. Finally, we address the importance of a systems perspective for understanding how genetic and epigenetic alterations map onto phenotypic changes by altering complex gene regulatory networks and affecting the evolution of plant phenotype, and discuss some of the technological approaches that could advance this field.