Histones are basic components of nucleosome and essential to chromatin structure and function. Histone posttranslational modifications and sequence variants jointly participate in modification of chromatin and regulation of gene expression. Histones are highly conserved proteins in different organisms. However, a high degree of variation was found in ciliate. In the study, H4A and H4B were cloned from Euplotes octocarinatus by PCR,GenBank accession number: JN715068 and JN715069. Sequences analysis showed that opening reading frame of the H4A gene was 324 bp, which encoded a 107 amino acid polypeptide with a predicted molecular mass of 11.6 ku and isoelectric point of 10.99. The opening reading frame of the H4B gene was 384 bp, which encoded a 127 amino acid polypeptide with a predicted molecular mass of 14.4 ku and isoelectric point of 9.93. H4A gene shared a high identity of 81%-94% with reported H4 gene, while H4B shared an identity of 36%-70% with H4 gene from other eukaryotes. H4A shared 44.7% identity with H4B. Real-time PCR showed that H4A transcript was higher than that of H4B. The results indicate that the H4 gene has different variants in E. octocarinatus.