The correct implementation of epigenetic mechanisms is often a prerequisite for the timely regulation of genome expression and structure and ultimately for the development of higher plants. Developmental regulation is thus playing a paramount role in the elaboration of yields in agricultural crops. However, numerous studies have shown that this tight control includes a certain degree of freedom as epigenetic regulations can be loosened in the course of the reproductive development, after hybridization or as part of the response to environmental constraints – both in vitro and in vivo – whereas genome stability is globally maintained. As a result, several modifi ed epigenetic marks and associated altered gene or transposable element expression can eventually give rise to qualitative or quantitative phenotypic changes on the long term. The present chapter is intended to present the main concepts governing epigenetic regulation of gene expression in higher plants and to review its potential applications for the selection of heritable phenotypes. It illustrates how epigenetic variations can be smartly used in breeding schemes and which questions remain to be addressed in order to make such integration successful. The Next Generation Sequencing revolution has also impacted our approach of plant epigenetics as more genomes, epigenomes and transcriptomes and are made available for crop plants and the simplistic Arabidopsis model is being questioned.