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Background  After fertilization, the fusion of gametes results in the formation of totipotent zygote. During sperm-egg fusion, maternal factors participate in parental chromatin remodeling. H3.3 is a histone H3 variant that plays essential roles in mouse embryogenesis.    Methods  Here, we used transgenic early embryos expressing H3.3-eGFP or H2B-mCherry to elucidate changes of histone mobility.    Results  We used FRAP analysis to identify that maternally stored H3.3 has a more significant change than H2B during maternal-to-embryonic transition. We also found that H3.3 mobile fraction, which may be regulated by  de novo  H3.3 incorporation, reflects chromatin compaction of parental genomes in GV oocytes and early embryos.    Conclusions  Our results show that H3.3 kinetics in GV oocytes and early embryos is highly correlated with chromatin compaction status of parental genomes, indicating critical roles of H3.3 in higher-order chromatin organization.    Supplementary Information  The online version contains supplementary material available at 10.1186/s12958-021-00776-3.

H3.3 kinetics predicts chromatin compaction status of parental genomes in early embryos