Abstract: 【Objective】To analyze molecular evolution of histone acetylation modification related genes and expression changes of the genes in Pinctada fucata martensii after nucleus transplantation，and to make clear the function of histone acetylation modification on nucleus transplantation immunity，so as to provide theoretical and technical guidance for appropriate control of immune response to nucleus transplantation.【Method】 Whole genome identification of histone acetylase（HAT）and histone deacetylase（HDAC）related genes in 9 species including P. fucata martensii，Crassostrea gigas，Danio rerio and Homo sapiens was operated through bioinformatics methods，and molecular evolution of the genes was analyzed. Based on transcriptomes data already obtained，expression change of HAT and HDAC genes in P. fucata martensii after nucleus transplantation，and hemocyte histone H3/H4 acetylation level was determined using histone H3/ H4 total acetylation quantitative analysis kit.【Result】The numbers of HAT and HDAC gene families in the genomes of 9 species varied inobviously，and the most recent common ancestor（MRCA）included 9 genes from 8 HAT gene families and 22 genes from 19 HDAC gene families. P. fucata martensii genome contained 8 genes（2 GNAT-like genes and 6 MYST-like genes）from 2 HAT families（GNAT and MYST）；HAT gene family members contained 18 conserved amino acid sequences，and all existing MYST-like genes contained MOZ_SAS domain and GNAT-like genes contained Hat1_N or Acetyltransf_1 domains，indicating that the sequences were highly conserved. P. fucata martensii genome contained 18 genes from 13 HDAC gene families，including 3 genes in Class I，3 in Class II，10 in Class III and 2 in Class IV. HDAC Class III gene family contained 3 conserved amino acid sequences，and HDAC Class I/II/ IV gene families contained 21 conserved amino acid sequences，but they were distributed in different positions and had different sequence composition， indicating that the structure of the family members was diverse. HDAC Class III genes in P. fucata martensii，C. agigas， and H. sapiens contained from 1 to 2 SIR2 domains，and HDAC Class I/II/IV genes contained one or more Hist-deacety1 domains. Hemocytes transcriptome of P. fucata martensii contained all of the detected HDAC and HAT genes，and expression of HDAC genes changed dynamically after nucleus transplantation，but most expression of HAT genes did not change；acetylation modification level of histone H3 and histone H4 increased significantly at 6，12 and 24 h after nucleus transplantation in P. fucata martensii（P<0.05），and at 48 h，the acetylation level of histone H3 was still high，while the acetylation level of histone H4 returned to normal.【Conclusion】Genome copy number，domain composition and conserved amino acid sequence of histone acetylation related genes are conserved in different species，and histone acetylation modification is involved in regulation of immune response to nucleus transplantation in P. fucata martensii.