Basonuclin is a zinc finger protein specific to basal keratinocytes and germ cells. In keratinocytes, basonuclin behaves as a stem cell marker and is thought to be a transcription factor that maintains proliferative capacity and prevents terminal differentiation. The human gene is located on chromosome 15. We have discovered in the chicken the existence of basonuclin 2, a basonuclin homolog. We also report the entire sequence of mouse and human basonuclin 2; the corresponding genes are located on mouse chromosome 4 and human chromosome 9. Although the amino acid sequence of basonuclin 2 differs extensively from that of basonuclin 1, the two proteins share essential features. Both contain three paired zinc fingers, a nuclear localization signal, and a serine stripe. The basonuclin 2 mRNA has a wider tissue distribution than the basonuclin 1 mRNA: it is particularly abundant in testis, kidney, uterus, and intestine. The extreme conservation of the basonuclin 2 amino acid sequence across vertebrates suggests that basonuclin 2 serves an important function, presumably as a regulatory protein of DNA transcription.