Plant genomes are divided into euchromatin and heterochromatin, which generally corresponds to gene versus transposon rich regions. We now appreciate that epigenetic modifications of the genome, for example DNA methylation, underlie differentiation of the genome into these different chromatin states. In addition to associating with different patterns of transcription, it is known that plant heterochromatin is typically also silenced for recombination during meiosis. In many of the large grass genomes, including wheat, the majority of the chromosomes consist of non-recombining expanses of heterochromatin, which can cause significant limitations for breeding. Our research investigates the genetic and epigenetic factors that shape recombination in plant genomes. I will present new data where we have profiled Arabidopsis recombination factors genome-wide, which has revealed hotspots associated with genes and also, surprisingly, DNA transposons. I will discuss the implications of these finds for plant genome evolution and the relationship between genes and transposons. I will also present new work profiling chromatin states in the hexaploid wheat genome and show how this correlates with recombination. In summary I will explore the relationships between chromatin, transcription and recombination, with implications for the stability of plant chromosomes and how we improve crops via breeding.