Our understanding of the genetics of the muriqui have increased in recent decades. In the mid 1980’s the first data was obtained from polymorphisms of allozymes of 10 individuals of B. hypoxanthus (northern muriqui) from Minas Gerais, and two individuals of B. arachnoides (southern muriqui) from São Paulo. All specimens were considered to be of a single species. The DNA was extracted from blood samples, which required capture and anesthesia of animals. We can now extract mitochondrial DNA from feces samples. Analyzing more than 120 individuals of the northern muriqui from two populations, we are now able make inferences about genetic variability, population distinctiveness as well as intra- and interpopulation gene flow. DNA sampling through feces is reliable, efficient, and economic, and does not risk the physical integrity of the animals, and furnishes enough DNA that is easily reproducible for PCR amplification. Using this method it is possible to sample a greater number of individuals in nature than would be possible if live capture were necessary. A muriqui feces and DNA bank has been set up, and currently has samples of 230 individuals from seven of the twelve known populations of northern muriqui. The samples resulted from field studies, but more coordinated and systematic efforts among fieldworkers at the different muriqui sites are needed to improve representation across populations and species. Future perspectives include the use of new genetic markers (nuclear and mitochondrial DNA) to identify parents, offspring, and closely related individuals in captive and wild populations; to define units for conservation and the gene flow between them; to quantify genetic variability in the populations; to assess the rate at which genetic variation has been lost over time; to estimate the degree of inbreeding in the population; and to understand better the genetic differentiation of the two species.