Abstract: Histone H1 participates in the formation of high-level chromatin structure. In addition to structuralfunction, histone H1 also affects chromatin function and dynamics through the presence of post-translational histone modifications or specific histone variants, and has the ability to participate in biological immune responses and control cell proliferation and other functions. In this study, the histone H1 genes from 9 species, including Pinctada fucata martensii, Crassostrea gigas, and Homo sapiens et al., were identified and analyzed through construction of phylogenetic trees and multiple sequences alignment methods. The expression pattern of H1 gene during the development and after transplantation in Pinctada fucata martensii were re-analyzed to obtain its molecular evolution and functional differentiation characteristics in P.f.martensii. The results showed that the genome of Pinctada martensii contained 23 histone H1 gene variants, showing the specific expansion of the organism. Multi-sequence alignment analysis of the amino acid sequences of the histone H1 gene of Pinctada fucata martensii, Crassostrea gigas and Homo sapiens showed that the sequence of histone H1 was highly conserved among species. Twelve transcripts of histone H1 genes were detected in the transcriptomes at different developmental stages of P.f.martensii. Three histone H1 genes were found in gastrula, early trochophore, trochophore, D-larvae, D-shaped larvae before feeding, early umbo larvae, eye-larvae, post-veliger and juveniles. And one histone H1 gene was highly expressed in the egg stage and the fertilized egg stage. Histone H1 gene had formed different expression mechanisms in the course of evolution, resulting in functional differentiation, which was induced at different developmental stages to perform different functions. A total of 11 histone H1 genes were identified in the transcriptome of the hemocytes. After allograft and xenograft transplantation, the expression of 9 histone H1 genes increased significantly at 3 to 6 days, and 2 histone H1 genes were highly expressed at 6～12 h, and was basically recovered to the level before nucleation at 12 days, which further illustrated the functional differentiation characteristics of different histone H1 gene. The above results indicated that histone H1 had a specific expansion and functional differentiation in the P.f.martensii genome, and was involved in the regulation of the development and nuclear immune process of P.f.martensii. This study provides a theoretical basis for further exploring the function of histone H1 gene in P.f.martensii.