JMJD1 family genes, including JMJD1 (TSGA), TRIP8, and C5orf7 (5qNCA), encode nuclear proteins with Jumonji C (JmjC), TRI8H1 and TRI8H2 domains. Here, we identified JMJD2 family genes. Human genes corresponding to KIAA0677, KIAA0876, KIAA0780 and FLJ10251 cDNAs were designated JMJD2A, JMJD2B, JMJD2C, and JMJD2D, respectively. In addition, JMJD2D homologous genes within human genome sequences AP002383.3 and AP001264.4 were designated JMJD2E and JMJD2F, respectively. JMJD2A gene was mapped to human chromosome 1p34.1, JMJD2B gene to 19p13.3, and JMJD2C gene to 9p24.1. JMJD2D, JMJD2E and JMJD2F genes were clustered at human chromosome 11q21. Coding region of JMJD2A, JMJD2B, JMJD2C genes was located on multiple exons, while that of JMJD2D, JMJD2E and JMJD2F genes was located on a single exon. These facts strongly indicate that JMJD2D, JMJD2E and JMJD2F genes are locally triplicated retrotransposed elements derived from JMJD2 family gene. JD2H domain with C2HC2HC2- and C5HC2-type Cys (His) clusters was identified as the region conserved among JMJD2A (1064 aa), JMJD2B (1096 aa), and JMJD2C (1056 aa) proteins. JMJD2A, JMJD2B and JMJD2C consist of JmjN, JmjC, JD2H, and two TUDOR domains, while JMJD2D (523 aa), JMJD2E (506 aa) and JMJD2F (638 aa) consist of JmjN and JmjC domains. JMJD2 family proteins were classified into one group with JD2H and TUDOR domains and another group without JD2H or TUDOR domains. Because JMJD2C gene (also known as GASC1 gene) is amplified in esophageal squamous cell carcinoma (ESCC), JMJD2 family genes are cancer-associated genes. This is the first report on identification and characterization of human JMJD2 gene family.