The most commonly used non-human primates in medical research are of the genus Macaca, making it important to gain a better understanding of their genetic differences. The Macaca genus of Old World monkeys is closely related to humans, sharing a last common ancestor ~25 million years ago (Mya) . The close relationship between humans and macaques has made several species attractive as animal models for a variety of different biomedical analyses, including investigations of cancer, neurological disease, HIV infection, Parkinson’s disease, malaria, drug abuse, as well as in toxicology and vaccine and drug testing. Although the Indian subspecies of the rhesus macaque (Macaca mulatta mulatta) was originally the research model of choice, a ban on the export of this rhesus macaque has greatly reduced the availability of these animals, leading to increased use of other macaque species/subspecies, in particular the Chinese rhesus macaque (Macaca mulatta lasiota) and the cynomolgus/crab-eating macaque (Macaca fascicularis). Here we present genome information of two newly sequenced macaca: the Chinese rhesus macaque and the cynomolgus/crab-eating macaque and a previously sequenced the Indian rhesus macaque. Together with the expression information of Indian rhesus macaque and cynomolgus/crab-eating macaque, we want to distinguish the difference of rhesus and cynomolgus as model animal.