Histone H3.3, a gene that is differentially expressed in the vegetative cell of lily pollen, was characterized immunologically. Antibody raised against a specific peptide fragment clearly recognized histone H3.3 in mature pollen, and did not cross-react with somatic histone H3s. Immunoblot analysis indicated that the variant histone H3.3 increased during the development of late-bicellular pollen to mature pollen. Immunofluorescence labeling of pollen grains using the specific antibody revealed the presence of variant histone H3.3 only in the vegetative cell nucleus and not in the generative cell nucleus. This is the first study to demonstrate a differentially expressed variant histone H3.3 present in the vegetative cell nucleus. Since the chromatin of the vegetative cell nucleus is largely diffuse and transcriptionally active, the accumulation of a specialized histone H3.3 in the vegetative cell nucleus may potentially control condensation of chromatin and regulate the upregulation of pollen-enhanced genes expressed in the course of pollen germination and tube growth.