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The Neotropics contributes significantly to global biodiversity yet little is known about its mammalian fauna. Given our limited knowledge, concerns are that extinctions at the local level may cause a decline in genetic diversity through the loss of unique alleles. Here we report the geographical population structure of four rodent species from French Guiana: Dasyprocta leporina, Agouti paca, Proechimys cayennensis and P. cuvieri. Two of them ( Dasyprocta and Agouti) are commonly harvested throughout the country for subsistence and/or game hunting. Cytochrome b and control region sequences revealed the presence of a number of maternal lineages occurring in sympatry throughout French Guiana. We applied two cytochrome b rodent clock calibrations (7.5% and 12% per million years) to our data, and placed the divergence of the maternal lineages to between 160 000 and 260 000 years ago for the more diverse D. leporina and P. cuvieri, and between 66 000 and 46 000 years ago for the more recent A. paca and P. cayennensis. The clades appear to be widespread throughout South America as indicated by specimens sampled in Brazil, Peru, and Venezuela. At the population level, AMOVA revealed little or no geographical structure within French Guiana. However, this conclusion is based on a single genetic marker and relatively few specimens. © 2004 The Linnean Society of London, Biological Journal of the Linnean Society, 2004, 81, 203–218. [ABSTRACT FROM AUTHOR]