We used the mitochondrial cytochrome b gene to study the population genetic structure of Melanosuchus niger (Brazil: Negro and Purus Rivers, Lake Janauacá; French Guiana: Kaw River swamps), and Caiman crocodilus (Brazil: Purus River, Lake Janauacá; French Guiana: Kaw River swamps). We found 10 haplotypes in M. niger and 9 haplotypes in C. crocodilus. Nested clade analysis indicated that isolation-by-distance was an important population dynamic in M. niger, but was unable to differentiate between isolation-by-distance, historical fragmentation or range expansion in C. crocodilus. Fu's Fs statistic supported the hypothesis of a demographic expansion in one out of four and two out of three sampled localities of M. niger and C. crocodilus, respectively. Populations of M. niger in central Amazonia also appeared to show differentiation that was correlated with water type. These results are compatible with the life-style of these two crocodilians; C. crocodilus is a habitat generalist and appears to disperse rapidly to newly available habitats, while M. niger is a more sedentary habitat specialist. Both species appear to be recovering from unregulated over-harvesting, however, their responses are life-history and, potentially, ecologically-dependent.