The determination of genetic parameters for most waterbird populations presents considerable challenges because these species frequently breed in inaccessible locations which preclude capture of nesting pairs. The application of non-invasive sampling techniques, such as the collection of molted feathers in the field, could represent an appealing strategy to overcome the above cited problem. Here, the feasibility of sampling molted feathers collected in Brazilian populations of the Roseate Spoonbill (Platalea ajaja; N = 94) and the jabiru Stork (Jabiru mycteria; N = 10) for genetic studies was evaluated. Each feather yielded high quality DNA with a concentration 1.25 times higher than that obtained from feathers from similar sized birds from other groups. Amplification of a 390– 396 bp fragment for molecular sexing and 11 microsatellite loci was successful. The average percentage of positive PCRs (i.e. those that yielded products) among all Roseate Spoonbill loci and samples was 95.5%. The sampling approach appears suitable to gather genetic information in natural populations of these waterbirds and can be applied to other similar species.