The nucleosome, composed of DNA and a histone core, is the basic structural unit of chromatin. The fission yeast Schizosaccharomyces pombe has two genes of histone H2A, hta1 +  and hta2 + ; these genes encode two protein species of histone H2A (H2Aα and H2Aβ, respectively), which differ in three amino acid residues, and only hta2 +  is upregulated during meiosis. However, it is unknown whether S. pombe H2Aα and H2Aβ have functional differences. Therefore, in this study, we examined the possible functional differences between H2Aα and H2Aβ during meiosis in S. pombe. We found that deletion of hta2 + , but not hta1 + , causes defects in chromosome segregation and spore formation during meiosis. Meiotic defects in hta2 +  deletion cells were rescued by expressing additional copies of hta1 +  or by expressing hta1 +  from the hta2 promoter. This indicated that the defects were caused by insufficient amounts of histone H2A, and not by the amino acid residue differences between H2Aα and H2Aβ. Microscopic observation attributed the chromosome segregation defects to anaphase bridge formation in a chromosomal region at the repeats of ribosomal RNA genes (rDNA repeats). These results suggest that histone H2A insufficiency affects the chromatin structures of rDNA repeats, leading to chromosome missegregation in S. pombe.