Genome: Macaca fascicularis

Cynomolgus Macaque

Scientific Name
Macaca fascicularis
Common Name
Cynomolgus Macaque


Cynomolgus macaques (Macaca fascicularis) are a critically important nonhuman primate in biomedical research, used in large numbers by investigators in pharmacology, breast, uterine and other cancers, diabetes, cardiovascular disease, and other fields. Cynomolgus macaques are closely related to rhesus macaques (Macaca mulatta). While clearly distinct in body size (cynomolgus macaques are smaller), physiology, and susceptibility to infectious diseases, these two species can form reproductively viable hybrids in the wild.

Because they are relatively small in comparison to other Old World monkey laboratory species, cynomolgus macaques have been widely used in drug development, drug testing, and toxicology. They also show a valuable pattern of lipoprotein and other cardiovascular responses to dietary cholesterol, dietary fat, and other risk factors. This species is highly responsive to stress, and thus has frequently been used to test interactions between stress and other cardiovascular risk factors. Diabetes is also characteristic of a significant fraction of cynomolgus monkeys, and this has been exploited by numerous investigators. Estrogen physiology, the effects of psychosocial stress on reproductive function, and the interactions of estrogens with dietary and other risk factors for disease have all been studied in this species. Finally, cynomolgus macaques have received significant attention as models for drug abuse, alcohol abuse, depression, and other psychiatric/psychological disorders.


The cynomolgus, or crab-eating macaque (Macaca fascicularis) is native to Southeast Asia. They are widely distributed in Malaysia, Indonesia and the Philippines. They inhabit tropical forests, but are quite tolerant of captive housing and diets. There are several major breeding colonies in the U.S., but large numbers of these animals can be imported from Indonesia and other sources, making them readily available to laboratories at much lower cost than rhesus monkeys.

Sequencing Plan

The impact of whole-genome sequencing of the cynomolgus macaque is significant. Accurate information about gene content and the specific sequences for cynomolgus genes would improve opportunities for studies of pharmacology and pharmacogenomics, responses to infectious disease, and metabolic disorders such as diabetes and osteoporosis. While cynomolgus macaques are closely related to rhesus, differences in gene number and sequences mean that quantitative studies of gene expression may benefit from species-specific genomic data. Given their small size, lower cost, and more convenient handling, use of this species would likely increase, if sophisticated analyses and tools based on state-of-the-art genomic data were available. Expansion of the diversity of primate species used for biomedical research is a goal within the NIH, given the high cost of overdependence on rhesus macaques.

Genetic, morphological, and physiological differences among populations of cynomolgus macaques are significant, and becoming well-known. This species is well-suited to detailed studies of genomic variation, the phenotypic consequences of genetic variation, and the consequences of selection on the primate genome. While closely related to the rhesus macaque, there are biologically meaningful differences in physiology, especially susceptibility to infectious disease. Therefore, detailed comparison of these two species of macaques at the physiological, cellular, and genomic levels would provide insight into both mechanisms of disease and primate responses to selection and the neutral forces of evolution.

-Excerpts taken from the NHGRI whitepaper.


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Data Links

Species Name Data Type
Macaca fascicularis NCBI Genome Page Link
Macaca fascicularis NCBI BioProject ID Link