The evolutionary changes in the Drosophila H2A and H2AvD genes, which encode histones, were analyzed using the sequences of 12 Drosophila sp. for understanding the evolution of histone replacement and epigenetics. The Ball gene, coding for a histone threonine kinase, was located head-to-head with the H2AvD gene in seven Drosophila sp. A strongly conserved DNA sequence was also found in the region upstream of the H2AvD gene; this sequence is most likely a transcriptional signal, because the sequence was also conserved in four other Drosophila sp. that did not have an upstream Ball gene. The SPARC gene, coding for a calcium-binding domain, was located tail-to-tail in the region downstream of the H2AvD gene in 11 Drosophila sp. studied. A moderately conserved DNA sequence was found in the H2AvD gene region at the splicing site in the first intron. Different codon usages for the H2A and H2AvD genes were found for 11 of 17 amino acids, and codon usages characteristic of replacement histones (H2AvD, H4r, H3.3A and H3.3B) were found for amino acids. Codon usage was considerably different at several histone modification sites in the H2A gene. These results suggested that unlike the H3.3 and H4r genes, not only post-transcriptional control, but also transcriptional control played a role in the H2AvD gene. In addition to post-transcriptional controls, such as splicing and translation, the development of a control system for transcription must have occurred during the evolution of histone replacement and epigenetic systems.