In 2004, an unidentified disease causing chlorotic yellows on the leaves of melon (Cucumis melo) plants was found in Kumamoto Prefecture. A few flexuous filamentous structures (ca. 900 nm in length) were observed with transmission electron microscopy. RT-PCR and subsequent nested PCR amplified a DNA fragment, which had 75% and 73% similarities with a corresponding sequence for Cucurbit yellow stunting disorder virus and Beet pseudo-yellows virus, respectively. Both Bemisia tabaci Q-biotype and B. tabaci B-biotype (syn. B. argentifolii) acquired and transmitted the virus, and the infected melon plants developed the original symptoms of the disease. These results demonstrate that the virus is a new species in the genus Crinivirus (family Closteroviridae), and we propose the name Cucurbit chlorotic yellows virus.