Here we consider the phylogeography and population structure of the tucuxi dolphin Sotalia fluviatilis, based on samples (n= 26) collected across the Peruvian, Colombian and Brazilian Amazon Regions. Fourteen control region (CR) and two cytochrome b (Cyt-b) haplotypes were identified among these samples. The Amazonian population units identified showed high mitochondrial haplotype diversity and relatively high female mediated gene flow when compared to Sotalia guianensis and another Amazonian dolphin species, Inia geoffrensis