In eukaryotes, including yeasts, fungi, animals and plants, myo-inositol is used as a building block to generate derivatives by attaching multiple combinations of mono- and pyrophosphate groups to each of the hydroxyl moieties. During the past decade, genetic and cell biological advances have indicated that these inositol polyphosphates are involved in regulating fundamental cellular processes such as directed membrane trafficking, protein structure maintenance, ion channel regulation, mRNA transportation, DNA repair, and chromatin remodeling. In recent years, many genes involved in inositol phosphate metabolism have been identified to play important roles in Arabidopsis development and stress responses. This review describes the known Arabidopsis inositol polyphosphate kinases and phosphatases, the emerging roles of these small molecules as signaling codes to regulate the fundamental cellular processes in plants, and the research trends.