The São Pedro and São Paulo Archipelago (SPSPA) (00°56’N, 29°22’W) lies approximately 1010km northeast off the coast of Rio Grande do Norte State in Brazilian waters. Recently, through photo-identification and group size analysis, around 20-30 individual bottlenose dolphins, Tursiops truncatus, from SPSPA were recognized as a resident, and potentially genetically isolated, population. The effective population size (Ne), not the census number (Nc), as well the sex ratio, are of primary concern from an evolutionary and conservation management perspectives. The estimate of Ne reflects the number of individuals responsible for the maintenance of genetic diversity of a species or population as well its evolutionary potential. For this reason, we present here the first Ne and sex ratio estimates for the bottlenose dolphin population from SPSPA. Sex was molecularly determined for 19 biopsy samples collected from bottlenose dolphins from SPSPA between January and February 2005. The Newas estimated by direct counting of reproductive adults sexed by DNA analysis. The resulting Ne was 12 individuals and the sex ratio was 1.11 male to 1 female, however, it was not significantly different from the expected 1:1 ratio (χ2 test, α= 0.05; df = 1). The effective population size based on the genetic diversity of 19 sequences of the mtDNA control region resulted in a female effective population size of 223 individuals, and the total long-term effective size of ~470 individuals. We believe that the estimated Ne for the SPSPA population is a critical value, because it is significantly lower than the mean minimum viable population (MVP) suggested for vertebrates (around 5000 breeding age adults). This small Ne is of great concern and should be taken into account in future management plans to ensure the conservation and protection of this small population at SPSPA.