Eleven taxa of primates are found in the floodplains of the western portion of the central Brazilian Amazon, protected in part by the Mamiraua Sustainable Development Reserve. The taxonomy of the squirrel monkeys, the number of taxa, and their geographic distributions are still poorly understood. Here we investigate differentiation among the taxa of this genus in Mamiraua, examining their morphology and geographic distribution. We registered 333 points of occurrence of squirrel monkeys and examined 117 specimens deposited in scientific collections. The results of the morphological analyses were generally in good agreement with field observations. Together they indicate the existence of three taxa: Saimiri vanzolinii, Saimiri sciureus macrodon, and S. s. cassiquiarensis. The restricted range of Saimiri vanzolinii in the southeastern portion of the reserve covers an area of 870 km(2), and it is among the smallest of the distribution areas for any Neotropical primate species. Saimiri sciureus cassiquiarensis has a disjunct distribution, crossing the Japura River to the right bank into the reserve in two places, and S. s. macrodon is the squirrel monkey ranging widely in the northwest of Mamiraua. There are three areas of parapatry: one between Saimiri vanzolinii and Saimiri sciureus macrodon and two between S. vanzolinii and S. s. cassiquiarensis. We recommend that anthropogenic changes in the region be monitored, and conservation measures be taken to protect these primates, especially considering the endemism and very restricted range of Saimiri vanzolinii and its consequent vulnerability to extinction.