Covalent histone modifications and their effects on chromatin state and accessibility play a key role in the regulation of gene expression in eukaryotes. To gain insights into their functions during plant growth and development, the distribution of histone modifications can be analyzed at a genome-wide scale through chromatin immunoprecipitation assays followed by sequencing of the isolated genomic DNA. Here, we present a protocol for systematic analysis of the distribution and dynamic changes of selected histone modifications, during flower development in the model plant Arabidopsis thaliana. This protocol utilizes a previously established floral induction system to synchronize flower development, which allows the collection of sufficient plant material for analysis by genomic technologies. In this chapter, we describe how to use this system to study, from the same set of samples, chromatin and transcriptome dynamics during early stages of flower formation.